diff --git a/src/meta/src/barrier/command.rs b/src/meta/src/barrier/command.rs
index 04b8fed711dd..e86c512a1ccd 100644
--- a/src/meta/src/barrier/command.rs
+++ b/src/meta/src/barrier/command.rs
@@ -522,14 +522,8 @@ impl CommandContext {
                 }
 
                 Command::SourceSplitAssignment(change) => {
-                    let mut checked_assignment = change.clone();
-                    checked_assignment
-                        .iter_mut()
-                        .for_each(|(_, assignment)| validate_assignment(assignment));
-
                     let mut diff = HashMap::new();
-
-                    for actor_splits in checked_assignment.values() {
+                    for actor_splits in change.values() {
                         diff.extend(actor_splits.clone());
                     }
 
@@ -581,7 +575,11 @@ impl CommandContext {
                     let mut checked_split_assignment = split_assignment.clone();
                     checked_split_assignment
                         .iter_mut()
-                        .for_each(|(_, assignment)| validate_assignment(assignment));
+                        .for_each(|(_, assignment)| {
+                            // No related actor running before, we don't need to check the mutation
+                            // should be wrapped with pause.
+                            validate_assignment(assignment);
+                        });
                     let actor_splits = checked_split_assignment
                         .values()
                         .flat_map(build_actor_connector_splits)
@@ -789,7 +787,8 @@ impl CommandContext {
 
                     for reschedule in reschedules.values() {
                         let mut checked_assignment = reschedule.actor_splits.clone();
-                        validate_assignment(&mut checked_assignment);
+                        // Update mutation always wrapped by Pause and Resume mutation. no further action needed.
+                        _ = validate_assignment(&mut checked_assignment);
 
                         for (actor_id, splits) in &checked_assignment {
                             actor_splits.insert(
diff --git a/src/meta/src/stream/source_manager.rs b/src/meta/src/stream/source_manager.rs
index a383bfee8e46..f900c7b6f2f0 100644
--- a/src/meta/src/stream/source_manager.rs
+++ b/src/meta/src/stream/source_manager.rs
@@ -588,21 +588,24 @@ where
     )
 }
 
-pub fn validate_assignment(assignment: &mut HashMap<ActorId, Vec<SplitImpl>>) {
+pub fn validate_assignment(assignment: &mut HashMap<ActorId, Vec<SplitImpl>>) -> bool {
+    let mut dup_assignment_found_flag = false;
+
     // check if one split is assign to multiple actors
     let mut split_to_actor = HashMap::new();
     for (actor_id, splits) in &mut *assignment {
-        let _ = splits.iter().map(|split| {
+        for split in splits {
             split_to_actor
                 .entry(split.id())
                 .or_insert_with(Vec::new)
-                .push(*actor_id)
-        });
+                .push(*actor_id);
+        }
     }
 
     for (split_id, actor_ids) in &mut split_to_actor {
         if actor_ids.len() > 1 {
             tracing::warn!(split_id = ?split_id, actor_ids = ?actor_ids, "split is assigned to multiple actors");
+            dup_assignment_found_flag = true;
         }
         // keep the first actor and remove the rest from the assignment
         for actor_id in actor_ids.iter().skip(1) {
@@ -612,6 +615,8 @@ pub fn validate_assignment(assignment: &mut HashMap<ActorId, Vec<SplitImpl>>) {
                 .retain(|split| split.id() != *split_id);
         }
     }
+
+    dup_assignment_found_flag
 }
 
 fn align_backfill_splits(
@@ -1100,15 +1105,28 @@ impl SourceManager {
     /// The command will first updates `SourceExecutor`'s splits, and finally calls `Self::apply_source_change`
     /// to update states in `SourceManager`.
     async fn tick(&self) -> MetaResult<()> {
-        let split_assignment = {
+        let mut split_assignment = {
             let core_guard = self.core.lock().await;
             core_guard.reassign_splits().await?
         };
 
+        let dup_assignment_flag = split_assignment
+            .iter_mut()
+            .map(|(_, assignment)| validate_assignment(assignment))
+            .reduce(|a, b| a || b)
+            .unwrap_or(false);
+
         if !split_assignment.is_empty() {
             let command = Command::SourceSplitAssignment(split_assignment);
             tracing::info!(command = ?command, "pushing down split assignment command");
-            self.barrier_scheduler.run_command(command).await?;
+            if dup_assignment_flag {
+                tracing::warn!("duplicate split assignment found, wrap with pause and resume");
+                self.barrier_scheduler
+                    .run_config_change_command_with_pause(command)
+                    .await?;
+            } else {
+                self.barrier_scheduler.run_command(command).await?;
+            }
         }
 
         Ok(())
@@ -1317,10 +1335,12 @@ mod tests {
             1 => test_assignment,
         };
 
-        fragment_assignment.iter_mut().for_each(|(_, assignment)| {
-            validate_assignment(assignment);
-        });
-
+        let dup_assignment_flag = fragment_assignment
+            .iter_mut()
+            .map(|(_, assignment)| validate_assignment(assignment))
+            .reduce(|a, b| a || b)
+            .unwrap_or(false);
+        assert!(dup_assignment_flag);
         {
             let mut split_to_actor = HashMap::new();
             for actor_to_splits in fragment_assignment.values() {