diff --git a/api/dify_graph/runtime/variable_pool.py b/api/dify_graph/runtime/variable_pool.py
index a2b1af99bb..e3ef6a2897 100644
--- a/api/dify_graph/runtime/variable_pool.py
+++ b/api/dify_graph/runtime/variable_pool.py
@@ -65,9 +65,15 @@ class VariablePool(BaseModel):
         # Add environment variables to the variable pool
         for var in self.environment_variables:
             self.add((ENVIRONMENT_VARIABLE_NODE_ID, var.name), var)
-        # Add conversation variables to the variable pool
+        # Add conversation variables to the variable pool. When restoring from a serialized
+        # snapshot, `variable_dictionary` already carries the latest runtime values.
+        # In that case, keep existing entries instead of overwriting them with the
+        # bootstrap list.
         for var in self.conversation_variables:
-            self.add((CONVERSATION_VARIABLE_NODE_ID, var.name), var)
+            selector = (CONVERSATION_VARIABLE_NODE_ID, var.name)
+            if self._has(selector):
+                continue
+            self.add(selector, var)
         # Add rag pipeline variables to the variable pool
         if self.rag_pipeline_variables:
             rag_pipeline_variables_map: defaultdict[Any, dict[Any, Any]] = defaultdict(dict)
diff --git a/api/tests/unit_tests/core/workflow/entities/test_graph_runtime_state.py b/api/tests/unit_tests/core/workflow/entities/test_graph_runtime_state.py
index 0df4927697..22792eb5b3 100644
--- a/api/tests/unit_tests/core/workflow/entities/test_graph_runtime_state.py
+++ b/api/tests/unit_tests/core/workflow/entities/test_graph_runtime_state.py
@@ -4,8 +4,10 @@ from unittest.mock import MagicMock, patch
 
 import pytest
 
+from dify_graph.constants import CONVERSATION_VARIABLE_NODE_ID
 from dify_graph.model_runtime.entities.llm_entities import LLMUsage
 from dify_graph.runtime import GraphRuntimeState, ReadOnlyGraphRuntimeStateWrapper, VariablePool
+from dify_graph.variables.variables import StringVariable
 
 
 class StubCoordinator:
@@ -278,3 +280,17 @@ class TestGraphRuntimeState:
         assert restored_execution.started is True
 
         assert new_stub.state == "configured"
+
+    def test_snapshot_restore_preserves_updated_conversation_variable(self):
+        variable_pool = VariablePool(
+            conversation_variables=[StringVariable(name="session_name", value="before")],
+        )
+        variable_pool.add((CONVERSATION_VARIABLE_NODE_ID, "session_name"), "after")
+
+        state = GraphRuntimeState(variable_pool=variable_pool, start_at=time())
+        snapshot = state.dumps()
+        restored = GraphRuntimeState.from_snapshot(snapshot)
+
+        restored_value = restored.variable_pool.get((CONVERSATION_VARIABLE_NODE_ID, "session_name"))
+        assert restored_value is not None
+        assert restored_value.value == "after"