diff --git a/lightrag/operate.py b/lightrag/operate.py
index 10cb251e..e976a5b4 100644
--- a/lightrag/operate.py
+++ b/lightrag/operate.py
@@ -681,7 +681,13 @@ async def _rebuild_single_entity(
             "description": final_description,
             "entity_type": entity_type,
             "source_id": GRAPH_FIELD_SEP.join(chunk_ids),
-            "file_path": GRAPH_FIELD_SEP.join(file_paths)
+            "file_path": build_file_path(
+                current_entity.get("file_path", "").split(GRAPH_FIELD_SEP)
+                if current_entity.get("file_path")
+                else [],
+                [{"file_path": fp} for fp in file_paths],
+                entity_name,
+            )
             if file_paths
             else current_entity.get("file_path", "unknown_source"),
         }
@@ -894,7 +900,13 @@ async def _rebuild_single_relationship(
         "keywords": combined_keywords,
         "weight": weight,
         "source_id": GRAPH_FIELD_SEP.join(chunk_ids),
-        "file_path": GRAPH_FIELD_SEP.join([fp for fp in file_paths if fp])
+        "file_path": build_file_path(
+            current_relationship.get("file_path", "").split(GRAPH_FIELD_SEP)
+            if current_relationship.get("file_path")
+            else [],
+            [{"file_path": fp} for fp in file_paths if fp],
+            f"{src}-{tgt}",
+        )
         if file_paths
         else current_relationship.get("file_path", "unknown_source"),
     }
@@ -1100,12 +1112,7 @@ async def _merge_edges_then_upsert(
             + already_source_ids
         )
     )
-    file_path = GRAPH_FIELD_SEP.join(
-        set(
-            [dp["file_path"] for dp in edges_data if dp.get("file_path")]
-            + [fp for fp in already_file_paths if fp]
-        )
-    )
+    file_path = build_file_path(already_file_paths, edges_data, f"{src_id}-{tgt_id}")
 
     for need_insert_id in [src_id, tgt_id]:
         if not (await knowledge_graph_inst.has_node(need_insert_id)):