diff --git a/fe/fe-core/src/main/java/com/starrocks/alter/AlterJobV2.java b/fe/fe-core/src/main/java/com/starrocks/alter/AlterJobV2.java
index e10426c0ad589..96318342448f5 100644
--- a/fe/fe-core/src/main/java/com/starrocks/alter/AlterJobV2.java
+++ b/fe/fe-core/src/main/java/com/starrocks/alter/AlterJobV2.java
@@ -223,8 +223,12 @@ public long getWarehouseId() {
      */
     public synchronized void run() {
         if (isTimeout()) {
-            cancelHook(cancelImpl("Timeout"));
-            return;
+            bool cancelled = cancelImpl("Timeout");
+            cancelHook(cancelled);
+            if (cancelled) {
+                // If this job can't be cancelled, we should execute it.
+                return;
+            }
         }
 
         // create connectcontext
diff --git a/fe/fe-core/src/main/java/com/starrocks/alter/SchemaChangeHandler.java b/fe/fe-core/src/main/java/com/starrocks/alter/SchemaChangeHandler.java
index 2ff33e541d59c..0e62624e58f75 100644
--- a/fe/fe-core/src/main/java/com/starrocks/alter/SchemaChangeHandler.java
+++ b/fe/fe-core/src/main/java/com/starrocks/alter/SchemaChangeHandler.java
@@ -2110,7 +2110,7 @@ public AlterJobV2 createAlterMetaJob(AlterClause alterClause, Database db, OlapT
             long timeoutSecond = PropertyAnalyzer.analyzeTimeout(properties, Config.alter_table_timeout_second);
             alterMetaJob = new LakeTableAlterMetaJob(GlobalStateMgr.getCurrentState().getNextId(),
                     db.getId(),
-                    olapTable.getId(), olapTable.getName(), timeoutSecond,
+                    olapTable.getId(), olapTable.getName(), timeoutSecond * 1000 /* should be ms*/,
                     TTabletMetaType.ENABLE_PERSISTENT_INDEX, enablePersistentIndex, persistentIndexType);
         } else {
             // shouldn't happen