diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.spec.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.spec.tsx
index 59c0bc71c7..a645180445 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.spec.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.spec.tsx
@@ -5,6 +5,8 @@ import TreeContextMenu from './tree-context-menu'
 const mocks = vi.hoisted(() => ({
   clearSelection: vi.fn(),
   deselectAll: vi.fn(),
+  getNode: vi.fn(),
+  selectNode: vi.fn(),
   fileOperations: {
     fileInputRef: { current: null },
     folderInputRef: { current: null },
@@ -73,6 +75,7 @@ vi.mock('./node-menu', () => ({
 describe('TreeContextMenu', () => {
   beforeEach(() => {
     vi.clearAllMocks()
+    mocks.fileOperations.showDeleteConfirm = false
   })
 
   describe('Rendering', () => {
@@ -90,8 +93,13 @@ describe('TreeContextMenu', () => {
   describe('Interactions', () => {
     it('should clear selection and open root menu when blank area is right clicked', () => {
       render(
-        <TreeContextMenu treeRef={{ current: { deselectAll: mocks.deselectAll } as never }}>
-          <div>blank area</div>
+        <TreeContextMenu treeRef={{ current: { deselectAll: mocks.deselectAll, get: mocks.getNode } as never }}>
+          <div>
+            <div data-skill-tree-node-id="file-1" data-skill-tree-node-type="file" role="treeitem">
+              readme.md
+            </div>
+            <div>blank area</div>
+          </div>
         </TreeContextMenu>,
       )
 
@@ -103,6 +111,30 @@ describe('TreeContextMenu', () => {
       expect(screen.getByTestId('node-menu-context')).toHaveAttribute('data-node-id', ROOT_ID)
     })
 
+    it('should switch to item menu when a tree node is right clicked', () => {
+      mocks.getNode.mockReturnValue({ select: mocks.selectNode })
+
+      render(
+        <TreeContextMenu treeRef={{ current: { deselectAll: mocks.deselectAll, get: mocks.getNode } as never }}>
+          <div>
+            <div data-skill-tree-node-id="file-1" data-skill-tree-node-type="file" role="treeitem">
+              readme.md
+            </div>
+            <div>blank area</div>
+          </div>
+        </TreeContextMenu>,
+      )
+
+      fireEvent.contextMenu(screen.getByRole('treeitem'))
+
+      expect(mocks.getNode).toHaveBeenCalledWith('file-1')
+      expect(mocks.selectNode).toHaveBeenCalledTimes(1)
+      expect(mocks.clearSelection).not.toHaveBeenCalled()
+      expect(mocks.deselectAll).not.toHaveBeenCalled()
+      expect(screen.getByTestId('node-menu-context')).toHaveAttribute('data-type', 'file')
+      expect(screen.getByTestId('node-menu-context')).toHaveAttribute('data-node-id', 'file-1')
+    })
+
     it('should keep import modal mounted after root menu requests it', () => {
       render(
         <TreeContextMenu treeRef={{ current: { deselectAll: mocks.deselectAll } as never }}>
@@ -118,5 +150,22 @@ describe('TreeContextMenu', () => {
       fireEvent.click(screen.getByText(/close-import-modal/i))
       expect(screen.queryByTestId('import-skill-modal')).not.toBeInTheDocument()
     })
+
+    it('should keep delete confirmation dialog mounted for item context actions', () => {
+      mocks.fileOperations.showDeleteConfirm = true
+
+      render(
+        <TreeContextMenu treeRef={{ current: { get: mocks.getNode } as never }}>
+          <div data-skill-tree-node-id="file-1" data-skill-tree-node-type="file" role="treeitem">
+            readme.md
+          </div>
+        </TreeContextMenu>,
+      )
+
+      fireEvent.contextMenu(screen.getByRole('treeitem'))
+
+      expect(screen.getByText('workflow.skillSidebar.menu.fileDeleteConfirmTitle')).toBeInTheDocument()
+      expect(screen.getByText('workflow.skillSidebar.menu.fileDeleteConfirmContent')).toBeInTheDocument()
+    })
   })
 })
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
index 23bc4544b2..263e6c3565 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-context-menu.tsx
@@ -4,6 +4,16 @@ import type { TreeApi } from 'react-arborist'
 import type { TreeNodeData } from '../../type'
 import * as React from 'react'
 import { useState } from 'react'
+import { useTranslation } from 'react-i18next'
+import {
+  AlertDialog,
+  AlertDialogActions,
+  AlertDialogCancelButton,
+  AlertDialogConfirmButton,
+  AlertDialogContent,
+  AlertDialogDescription,
+  AlertDialogTitle,
+} from '@/app/components/base/ui/alert-dialog'
 import {
   ContextMenu,
   ContextMenuContent,
@@ -28,33 +38,68 @@ type TreeContextMenuProps = Omit<
   children: React.ReactNode
 }
 
+type MenuTarget = {
+  nodeId: string
+  type: typeof NODE_MENU_TYPE.ROOT | typeof NODE_MENU_TYPE.FOLDER | typeof NODE_MENU_TYPE.FILE
+}
+
+const defaultMenuTarget: MenuTarget = {
+  nodeId: ROOT_ID,
+  type: NODE_MENU_TYPE.ROOT,
+}
+
 const TreeContextMenu = ({
   treeRef,
   triggerRef,
   children,
   ...props
 }: TreeContextMenuProps) => {
+  const { t } = useTranslation('workflow')
   const storeApi = useWorkflowStore()
+  const [menuTarget, setMenuTarget] = useState<MenuTarget>(defaultMenuTarget)
   const [isImportModalOpen, setIsImportModalOpen] = useState(false)
 
   const handleContextMenu = React.useCallback((event: React.MouseEvent<HTMLDivElement>) => {
     const target = event.target as HTMLElement
-    if (target.closest('[role="treeitem"]'))
+    const nodeElement = target.closest<HTMLElement>('[data-skill-tree-node-id]')
+
+    if (!nodeElement) {
+      setMenuTarget(defaultMenuTarget)
+      treeRef.current?.deselectAll()
+      storeApi.getState().clearSelection()
+      return
+    }
+
+    const nodeId = nodeElement.dataset.skillTreeNodeId
+    const nodeType = nodeElement.dataset.skillTreeNodeType
+
+    if (!nodeId || (nodeType !== NODE_MENU_TYPE.FILE && nodeType !== NODE_MENU_TYPE.FOLDER))
       return
 
-    treeRef.current?.deselectAll()
-    storeApi.getState().clearSelection()
+    treeRef.current?.get(nodeId)?.select()
+    setMenuTarget({
+      nodeId,
+      type: nodeType,
+    })
   }, [storeApi, treeRef])
 
   const handleMenuClose = React.useCallback(() => {}, [])
   const fileOperations = useFileOperations({
-    nodeId: ROOT_ID,
+    nodeId: menuTarget.nodeId,
     treeRef,
     onClose: handleMenuClose,
   })
   const handleOpenImportSkills = React.useCallback(() => {
     setIsImportModalOpen(true)
   }, [])
+  const isRootTarget = menuTarget.type === NODE_MENU_TYPE.ROOT
+  const isFolderTarget = menuTarget.type === NODE_MENU_TYPE.FOLDER
+  const deleteConfirmTitle = isFolderTarget
+    ? t('skillSidebar.menu.deleteConfirmTitle')
+    : t('skillSidebar.menu.fileDeleteConfirmTitle')
+  const deleteConfirmContent = isFolderTarget
+    ? t('skillSidebar.menu.deleteConfirmContent')
+    : t('skillSidebar.menu.fileDeleteConfirmContent')
 
   return (
     <>
@@ -69,8 +114,8 @@ const TreeContextMenu = ({
         <ContextMenuContent popupClassName="min-w-[180px]">
           <NodeMenu
             menuType="context"
-            type={NODE_MENU_TYPE.ROOT}
-            nodeId={ROOT_ID}
+            type={menuTarget.type}
+            nodeId={menuTarget.nodeId}
             onClose={handleMenuClose}
             fileInputRef={fileOperations.fileInputRef}
             folderInputRef={fileOperations.folderInputRef}
@@ -82,10 +127,43 @@ const TreeContextMenu = ({
             onFolderChange={fileOperations.handleFolderChange}
             onRename={fileOperations.handleRename}
             onDeleteClick={fileOperations.handleDeleteClick}
-            onImportSkills={handleOpenImportSkills}
+            onImportSkills={isRootTarget ? handleOpenImportSkills : undefined}
           />
         </ContextMenuContent>
       </ContextMenu>
+      {!isRootTarget && (
+        <AlertDialog
+          open={fileOperations.showDeleteConfirm}
+          onOpenChange={(open) => {
+            if (!open)
+              fileOperations.handleDeleteCancel()
+          }}
+        >
+          <AlertDialogContent>
+            <div className="flex flex-col gap-2 p-6 pb-4">
+              <AlertDialogTitle className="text-text-primary title-2xl-semi-bold">
+                {deleteConfirmTitle}
+              </AlertDialogTitle>
+              <AlertDialogDescription className="text-text-secondary system-sm-regular">
+                {deleteConfirmContent}
+              </AlertDialogDescription>
+            </div>
+            <AlertDialogActions>
+              <AlertDialogCancelButton>
+                {t('operation.cancel', { ns: 'common' })}
+              </AlertDialogCancelButton>
+              <AlertDialogConfirmButton
+                disabled={fileOperations.isDeleting}
+                onClick={() => {
+                  void fileOperations.handleDeleteConfirm()
+                }}
+              >
+                {t('operation.confirm', { ns: 'common' })}
+              </AlertDialogConfirmButton>
+            </AlertDialogActions>
+          </AlertDialogContent>
+        </AlertDialog>
+      )}
       <ImportSkillModal
         isOpen={isImportModalOpen}
         onClose={() => setIsImportModalOpen(false)}
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-node.spec.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-node.spec.tsx
index 9547a4761c..282b923a06 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-node.spec.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-node.spec.tsx
@@ -241,17 +241,17 @@ describe('TreeNode', () => {
       expect(handlerMocks.handleDoubleClick).toHaveBeenCalled()
     })
 
-    it('should call keyboard handler and open context menu on tree item right click', () => {
+    it('should call keyboard handler and expose node metadata for the shared context menu host', () => {
       const props = buildProps({ id: 'file-1', name: 'readme.md', nodeType: 'file' })
 
       render(<TreeNode {...props} />)
 
       const treeItem = screen.getByRole('treeitem')
       fireEvent.keyDown(treeItem, { key: 'Enter' })
-      fireEvent.contextMenu(treeItem)
 
       expect(handlerMocks.handleKeyDown).toHaveBeenCalledTimes(1)
-      expect(screen.getByTestId('node-menu-context')).toHaveAttribute('data-type', 'file')
+      expect(treeItem).toHaveAttribute('data-skill-tree-node-id', 'file-1')
+      expect(treeItem).toHaveAttribute('data-skill-tree-node-type', 'file')
     })
 
     it('should attach folder drag handlers only when node is a folder', () => {
@@ -344,22 +344,4 @@ describe('TreeNode', () => {
       expect(storeActions.setDragOverFolderId).toHaveBeenCalledWith(null)
     })
   })
-
-  describe('Dialogs', () => {
-    it('should keep delete confirmation dialog mounted when requested by menu actions', () => {
-      fileOperationMocks.showDeleteConfirm = true
-      const props = buildProps({ id: 'file-1', name: 'readme.md', nodeType: 'file' })
-
-      render(<TreeNode {...props} />)
-
-      expect(screen.getByText('workflow.skillSidebar.menu.fileDeleteConfirmTitle')).toBeInTheDocument()
-      expect(screen.getByText('workflow.skillSidebar.menu.fileDeleteConfirmContent')).toBeInTheDocument()
-
-      fireEvent.click(screen.getByRole('button', { name: /common\.operation\.confirm/i }))
-      fireEvent.click(screen.getByRole('button', { name: /common\.operation\.cancel/i }))
-
-      expect(fileOperationMocks.handleDeleteConfirm).toHaveBeenCalledTimes(1)
-      expect(fileOperationMocks.handleDeleteCancel).toHaveBeenCalledTimes(1)
-    })
-  })
 })
diff --git a/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx b/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
index 3282fc33ac..834a05a2f7 100644
--- a/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
+++ b/web/app/components/workflow/skill/file-tree/tree/tree-node.tsx
@@ -5,20 +5,6 @@ import type { TreeNodeData } from '../../type'
 import * as React from 'react'
 import { useCallback, useEffect, useRef } from 'react'
 import { useTranslation } from 'react-i18next'
-import {
-  AlertDialog,
-  AlertDialogActions,
-  AlertDialogCancelButton,
-  AlertDialogConfirmButton,
-  AlertDialogContent,
-  AlertDialogDescription,
-  AlertDialogTitle,
-} from '@/app/components/base/ui/alert-dialog'
-import {
-  ContextMenu,
-  ContextMenuContent,
-  ContextMenuTrigger,
-} from '@/app/components/base/ui/context-menu'
 import {
   DropdownMenu,
   DropdownMenuContent,
@@ -26,6 +12,7 @@ import {
 } from '@/app/components/base/ui/dropdown-menu'
 import { useStore, useWorkflowStore } from '@/app/components/workflow/store'
 import { cn } from '@/utils/classnames'
+import { NODE_MENU_TYPE } from '../../constants'
 import { useFolderFileDrop } from '../../hooks/file-tree/dnd/use-folder-file-drop'
 import { useTreeNodeHandlers } from '../../hooks/file-tree/interaction/use-tree-node-handlers'
 import { useFileOperations } from '../../hooks/file-tree/operations/use-file-operations'
@@ -95,129 +82,97 @@ const TreeNode = ({ node, style, dragHandle, treeChildren }: TreeNodeProps) => {
     e.stopPropagation()
   }, [])
 
-  const handleContextMenu = useCallback((e: React.MouseEvent) => {
-    e.stopPropagation()
-    node.select()
-  }, [node])
-
   const handleMenuClose = useCallback(() => {}, [])
   const fileOperations = useFileOperations({
     nodeId: node.data.id,
     node,
     onClose: handleMenuClose,
   })
-  const deleteConfirmTitle = isFolder
-    ? t('skillSidebar.menu.deleteConfirmTitle')
-    : t('skillSidebar.menu.fileDeleteConfirmTitle')
-  const deleteConfirmContent = isFolder
-    ? t('skillSidebar.menu.deleteConfirmContent')
-    : t('skillSidebar.menu.fileDeleteConfirmContent')
 
   return (
-    <>
-      <ContextMenu>
-        <ContextMenuTrigger
-          ref={dragHandle}
-          style={style}
-          role="treeitem"
-          tabIndex={0}
-          aria-selected={isSelected}
-          aria-expanded={isFolder ? node.isOpen : undefined}
-          className={cn(
-            'group relative flex h-6 cursor-pointer items-center rounded-md px-2',
-            'hover:bg-state-base-hover data-[popup-open]:bg-state-base-hover',
-            'focus-visible:outline-none focus-visible:ring-2 focus-visible:ring-inset focus-visible:ring-components-input-border-active',
-            isSelected && 'bg-state-base-active',
-            isDragOver && 'bg-state-accent-hover ring-1 ring-inset ring-state-accent-solid',
-            isBlinking && 'animate-drag-blink',
-            (isCut || node.isDragging) && 'opacity-50',
-          )}
-          onKeyDown={handleKeyDown}
-          onContextMenu={handleContextMenu}
-          {...(isFolder && {
-            onDragEnter: dragHandlers.onDragEnter,
-            onDragOver: dragHandlers.onDragOver,
-            onDrop: dragHandlers.onDrop,
-            onDragLeave: dragHandlers.onDragLeave,
-          })}
-        >
-          <TreeGuideLines level={node.level} />
-          <div
-            className="flex min-w-0 flex-1 items-center gap-2"
-            onClick={handleClick}
-            onDoubleClick={handleDoubleClick}
-          >
-            <div className="flex size-5 shrink-0 items-center justify-center">
-              <TreeNodeIcon
-                isFolder={isFolder}
-                isOpen={node.isOpen}
-                fileName={node.data.name}
-                extension={node.data.extension}
-                isDirty={isDirty}
-                onToggle={handleToggle}
-              />
-            </div>
+    <div
+      ref={dragHandle}
+      style={style}
+      role="treeitem"
+      tabIndex={0}
+      aria-selected={isSelected}
+      aria-expanded={isFolder ? node.isOpen : undefined}
+      data-skill-tree-node-id={node.data.id}
+      data-skill-tree-node-type={isFolder ? NODE_MENU_TYPE.FOLDER : NODE_MENU_TYPE.FILE}
+      className={cn(
+        'group relative flex h-6 cursor-pointer items-center rounded-md px-2',
+        'hover:bg-state-base-hover',
+        'focus-visible:outline-none focus-visible:ring-2 focus-visible:ring-inset focus-visible:ring-components-input-border-active',
+        isSelected && 'bg-state-base-active',
+        isDragOver && 'bg-state-accent-hover ring-1 ring-inset ring-state-accent-solid',
+        isBlinking && 'animate-drag-blink',
+        (isCut || node.isDragging) && 'opacity-50',
+      )}
+      onKeyDown={handleKeyDown}
+      {...(isFolder && {
+        onDragEnter: dragHandlers.onDragEnter,
+        onDragOver: dragHandlers.onDragOver,
+        onDrop: dragHandlers.onDrop,
+        onDragLeave: dragHandlers.onDragLeave,
+      })}
+    >
+      <TreeGuideLines level={node.level} />
+      <div
+        className="flex min-w-0 flex-1 items-center gap-2"
+        onClick={handleClick}
+        onDoubleClick={handleDoubleClick}
+      >
+        <div className="flex size-5 shrink-0 items-center justify-center">
+          <TreeNodeIcon
+            isFolder={isFolder}
+            isOpen={node.isOpen}
+            fileName={node.data.name}
+            extension={node.data.extension}
+            isDirty={isDirty}
+            onToggle={handleToggle}
+          />
+        </div>
 
-            {node.isEditing
-              ? (
-                  <TreeEditInput node={node} />
-                )
-              : (
-                  <span
-                    className={cn(
-                      'min-w-0 flex-1 truncate text-[13px] font-normal leading-4',
-                      isSelected
-                        ? 'text-text-primary'
-                        : 'text-text-secondary',
-                    )}
-                  >
-                    {node.data.name}
-                  </span>
+        {node.isEditing
+          ? (
+              <TreeEditInput node={node} />
+            )
+          : (
+              <span
+                className={cn(
+                  'min-w-0 flex-1 truncate text-[13px] font-normal leading-4',
+                  isSelected
+                    ? 'text-text-primary'
+                    : 'text-text-secondary',
                 )}
-          </div>
+              >
+                {node.data.name}
+              </span>
+            )}
+      </div>
 
-          <DropdownMenu>
-            <DropdownMenuTrigger
-              type="button"
-              aria-label={t('skillSidebar.menu.moreActions')}
-              tabIndex={-1}
-              onClick={handleMoreClick}
-              className={cn(
-                'flex size-5 shrink-0 items-center justify-center rounded',
-                'invisible focus-visible:visible group-hover:visible data-[popup-open]:visible',
-                'hover:bg-state-base-hover-alt data-[popup-open]:bg-state-base-hover-alt',
-                'focus-visible:outline-none focus-visible:ring-2 focus-visible:ring-components-input-border-active',
-              )}
-            >
-              <span className="i-ri-more-fill size-4 text-text-tertiary" aria-hidden="true" />
-            </DropdownMenuTrigger>
-            <DropdownMenuContent
-              placement="bottom-start"
-              sideOffset={4}
-              popupClassName="min-w-[180px]"
-            >
-              <NodeMenu
-                menuType="dropdown"
-                type={isFolder ? 'folder' : 'file'}
-                nodeId={node.data.id}
-                onClose={handleMenuClose}
-                fileInputRef={fileOperations.fileInputRef}
-                folderInputRef={fileOperations.folderInputRef}
-                isLoading={fileOperations.isLoading}
-                onDownload={fileOperations.handleDownload}
-                onNewFile={fileOperations.handleNewFile}
-                onNewFolder={fileOperations.handleNewFolder}
-                onFileChange={fileOperations.handleFileChange}
-                onFolderChange={fileOperations.handleFolderChange}
-                onRename={fileOperations.handleRename}
-                onDeleteClick={fileOperations.handleDeleteClick}
-              />
-            </DropdownMenuContent>
-          </DropdownMenu>
-        </ContextMenuTrigger>
-        <ContextMenuContent popupClassName="min-w-[180px]">
+      <DropdownMenu>
+        <DropdownMenuTrigger
+          type="button"
+          aria-label={t('skillSidebar.menu.moreActions')}
+          tabIndex={-1}
+          onClick={handleMoreClick}
+          className={cn(
+            'flex size-5 shrink-0 items-center justify-center rounded',
+            'invisible focus-visible:visible group-hover:visible data-[popup-open]:visible',
+            'hover:bg-state-base-hover-alt data-[popup-open]:bg-state-base-hover-alt',
+            'focus-visible:outline-none focus-visible:ring-2 focus-visible:ring-components-input-border-active',
+          )}
+        >
+          <span className="i-ri-more-fill size-4 text-text-tertiary" aria-hidden="true" />
+        </DropdownMenuTrigger>
+        <DropdownMenuContent
+          placement="bottom-start"
+          sideOffset={4}
+          popupClassName="min-w-[180px]"
+        >
           <NodeMenu
-            menuType="context"
+            menuType="dropdown"
             type={isFolder ? 'folder' : 'file'}
             nodeId={node.data.id}
             onClose={handleMenuClose}
@@ -232,40 +187,9 @@ const TreeNode = ({ node, style, dragHandle, treeChildren }: TreeNodeProps) => {
             onRename={fileOperations.handleRename}
             onDeleteClick={fileOperations.handleDeleteClick}
           />
-        </ContextMenuContent>
-      </ContextMenu>
-      <AlertDialog
-        open={fileOperations.showDeleteConfirm}
-        onOpenChange={(open) => {
-          if (!open)
-            fileOperations.handleDeleteCancel()
-        }}
-      >
-        <AlertDialogContent>
-          <div className="flex flex-col gap-2 p-6 pb-4">
-            <AlertDialogTitle className="text-text-primary title-2xl-semi-bold">
-              {deleteConfirmTitle}
-            </AlertDialogTitle>
-            <AlertDialogDescription className="text-text-secondary system-sm-regular">
-              {deleteConfirmContent}
-            </AlertDialogDescription>
-          </div>
-          <AlertDialogActions>
-            <AlertDialogCancelButton>
-              {t('operation.cancel', { ns: 'common' })}
-            </AlertDialogCancelButton>
-            <AlertDialogConfirmButton
-              disabled={fileOperations.isDeleting}
-              onClick={() => {
-                void fileOperations.handleDeleteConfirm()
-              }}
-            >
-              {t('operation.confirm', { ns: 'common' })}
-            </AlertDialogConfirmButton>
-          </AlertDialogActions>
-        </AlertDialogContent>
-      </AlertDialog>
-    </>
+        </DropdownMenuContent>
+      </DropdownMenu>
+    </div>
   )
 }