diff --git a/backend/packages/harness/deerflow/agents/middlewares/clarification_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/clarification_middleware.py
index 9e0c2b259..385508f0f 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/clarification_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/clarification_middleware.py
@@ -3,6 +3,7 @@
 import json
 import logging
 from collections.abc import Callable
+from hashlib import sha256
 from typing import override
 
 from langchain.agents import AgentState
@@ -36,6 +37,13 @@ class ClarificationMiddleware(AgentMiddleware[ClarificationMiddlewareState]):
 
     state_schema = ClarificationMiddlewareState
 
+    def _stable_message_id(self, tool_call_id: str, formatted_message: str) -> str:
+        """Build a deterministic message ID so retried clarification calls replace, not append."""
+        if tool_call_id:
+            return f"clarification:{tool_call_id}"
+        digest = sha256(formatted_message.encode("utf-8")).hexdigest()[:16]
+        return f"clarification:{digest}"
+
     def _is_chinese(self, text: str) -> bool:
         """Check if text contains Chinese characters.
 
@@ -131,6 +139,7 @@ class ClarificationMiddleware(AgentMiddleware[ClarificationMiddlewareState]):
         # Create a ToolMessage with the formatted question
         # This will be added to the message history
         tool_message = ToolMessage(
+            id=self._stable_message_id(tool_call_id, formatted_message),
             content=formatted_message,
             tool_call_id=tool_call_id,
             name="ask_clarification",
diff --git a/backend/tests/test_clarification_middleware.py b/backend/tests/test_clarification_middleware.py
index 9a8118996..565b09beb 100644
--- a/backend/tests/test_clarification_middleware.py
+++ b/backend/tests/test_clarification_middleware.py
@@ -1,8 +1,10 @@
 """Tests for ClarificationMiddleware, focusing on options type coercion."""
 
 import json
+from types import SimpleNamespace
 
 import pytest
+from langgraph.graph.message import add_messages
 
 from deerflow.agents.middlewares.clarification_middleware import ClarificationMiddleware
 
@@ -118,3 +120,60 @@ class TestFormatClarificationMessage:
         assert "2. 2" in result
         assert "3. True" in result
         assert "4. None" in result
+
+
+class TestClarificationCommandIdempotency:
+    """Clarification tool-call retries should not duplicate messages in state."""
+
+    def test_repeated_tool_call_uses_stable_message_id(self, middleware):
+        request = SimpleNamespace(
+            tool_call={
+                "name": "ask_clarification",
+                "id": "call-clarify-1",
+                "args": {
+                    "question": "Which environment should I use?",
+                    "clarification_type": "approach_choice",
+                    "options": ["dev", "prod"],
+                },
+            }
+        )
+
+        first = middleware.wrap_tool_call(request, lambda _req: pytest.fail("handler should not be called"))
+        second = middleware.wrap_tool_call(request, lambda _req: pytest.fail("handler should not be called"))
+
+        first_message = first.update["messages"][0]
+        second_message = second.update["messages"][0]
+
+        assert first_message.id == "clarification:call-clarify-1"
+        assert second_message.id == first_message.id
+        assert second_message.tool_call_id == first_message.tool_call_id
+
+        merged = add_messages(add_messages([], [first_message]), [second_message])
+
+        assert len(merged) == 1
+        assert merged[0].id == "clarification:call-clarify-1"
+        assert merged[0].content == first_message.content
+
+    def test_missing_tool_call_id_still_gets_stable_message_id(self, middleware):
+        request = SimpleNamespace(
+            tool_call={
+                "name": "ask_clarification",
+                "args": {
+                    "question": "Which environment should I use?",
+                    "clarification_type": "missing_info",
+                },
+            }
+        )
+
+        first = middleware.wrap_tool_call(request, lambda _req: pytest.fail("handler should not be called"))
+        second = middleware.wrap_tool_call(request, lambda _req: pytest.fail("handler should not be called"))
+
+        first_message = first.update["messages"][0]
+        second_message = second.update["messages"][0]
+
+        assert first_message.id.startswith("clarification:")
+        assert second_message.id == first_message.id
+
+        merged = add_messages(add_messages([], [first_message]), [second_message])
+
+        assert len(merged) == 1