diff --git a/paimon-flink/paimon-flink-common/src/main/java/org/apache/paimon/flink/clone/PickFilesForCloneOperator.java b/paimon-flink/paimon-flink-common/src/main/java/org/apache/paimon/flink/clone/PickFilesForCloneOperator.java
index f58d3acafdb9..512d48170f4a 100644
--- a/paimon-flink/paimon-flink-common/src/main/java/org/apache/paimon/flink/clone/PickFilesForCloneOperator.java
+++ b/paimon-flink/paimon-flink-common/src/main/java/org/apache/paimon/flink/clone/PickFilesForCloneOperator.java
@@ -25,6 +25,7 @@
 import org.apache.paimon.fs.Path;
 import org.apache.paimon.options.Options;
 import org.apache.paimon.schema.Schema;
+import org.apache.paimon.schema.SchemaManager;
 import org.apache.paimon.schema.TableSchema;
 import org.apache.paimon.table.FileStoreTable;
 import org.apache.paimon.utils.Preconditions;
@@ -85,6 +86,20 @@ public void processElement(StreamRecord<Tuple2<String, String>> streamRecord) th
         targetCatalog.createDatabase(targetIdentifier.getDatabaseName(), true);
         targetCatalog.createTable(
                 targetIdentifier, newSchemaFromTableSchema(sourceTable.schema()), true);
+        FileStoreTable targetTable = (FileStoreTable) targetCatalog.getTable(targetIdentifier);
+
+        // Make sure that latest schema file of source and target table are the same,
+        // so latest schema won't be overwritten in `CopyFileOperator` and the target table can
+        // always be retrieved from catalog.
+        SchemaManager sourceSchemaManager = sourceTable.schemaManager();
+        SchemaManager targetSchemaManager = targetTable.schemaManager();
+        long schemaId = sourceTable.schema().id();
+        targetTable
+                .fileIO()
+                .copyFile(
+                        sourceSchemaManager.toSchemaPath(schemaId),
+                        targetSchemaManager.toSchemaPath(schemaId),
+                        true);
 
         List<CloneFileInfo> result =
                 toCloneFileInfos(