diff --git a/src/copaw/agents/model_factory.py b/src/copaw/agents/model_factory.py
index 609b99f90..536cd24c2 100644
--- a/src/copaw/agents/model_factory.py
+++ b/src/copaw/agents/model_factory.py
@@ -11,7 +11,7 @@
 
 
 import logging
-from typing import Optional, Sequence, Tuple, Type, Any
+from typing import List, Sequence, Tuple, Type, Any, Union, Optional
 
 from agentscope.formatter import FormatterBase, OpenAIChatFormatter
 from agentscope.model import ChatModelBase, OpenAIChatModel
@@ -77,6 +77,7 @@ def _get_formatter_for_chat_model(
     )
 
 
+# pylint: disable-next=too-many-statements
 def _create_file_block_support_formatter(
     base_formatter_class: Type[FormatterBase],
 ) -> Type[FormatterBase]:
@@ -136,32 +137,44 @@ async def _format(self, msgs):
                             tc["extra_content"] = ec
 
             if reasoning_contents:
-                in_assistant = [m for m in msgs if m.role == "assistant"]
+                # Build a list of reasoning values aligned with surviving
+                # assistant messages.  The parent formatter drops
+                # thinking-only messages (no content/tool_calls), so we
+                # predict survivors and collect reasoning only for those.
+                aligned_reasoning = []
+                for m in (msg for msg in msgs if msg.role == "assistant"):
+                    is_thinking_only = (
+                        isinstance(m.content, list)
+                        and m.content
+                        and all(b.get("type") == "thinking" for b in m.content)
+                    )
+                    if not is_thinking_only:
+                        aligned_reasoning.append(
+                            reasoning_contents.get(id(m)),
+                        )
+
                 out_assistant = [
                     m for m in messages if m.get("role") == "assistant"
                 ]
-                if len(in_assistant) != len(out_assistant):
+
+                if len(aligned_reasoning) != len(out_assistant):
                     logger.warning(
                         "Assistant message count mismatch after formatting "
-                        "(%d before, %d after). "
+                        "(%d expected survivors, %d actual). "
                         "Skipping reasoning_content injection.",
-                        len(in_assistant),
+                        len(aligned_reasoning),
                         len(out_assistant),
                     )
                 else:
-                    for in_msg, out_msg in zip(
-                        in_assistant,
-                        out_assistant,
-                    ):
-                        reasoning = reasoning_contents.get(id(in_msg))
-                        if reasoning:
-                            out_msg["reasoning_content"] = reasoning
+                    for i, out_msg in enumerate(out_assistant):
+                        if aligned_reasoning[i]:
+                            out_msg["reasoning_content"] = aligned_reasoning[i]
 
             return _strip_top_level_message_name(messages)
 
         @staticmethod
         def convert_tool_result_to_string(
-            output: str | list[dict],
+            output: Union[str, List[dict]],
         ) -> tuple[str, Sequence[Tuple[str, dict]]]:
             """Extend parent class to support file blocks.