diff --git a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/CatalogMetaMapper.java b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/CatalogMetaMapper.java
index 652cf52cadd..038b4256f0b 100644
--- a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/CatalogMetaMapper.java
+++ b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/CatalogMetaMapper.java
@@ -137,14 +137,14 @@ Integer updateCatalogMeta(
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE catalog_id = #{catalogId} AND deleted_at = 0")
   Integer softDeleteCatalogMetasByCatalogId(@Param("catalogId") Long catalogId);
 
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE metalake_id = #{metalakeId} AND deleted_at = 0")
   Integer softDeleteCatalogMetasByMetalakeId(@Param("metalakeId") Long metalakeId);
 }
diff --git a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/FilesetMetaMapper.java b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/FilesetMetaMapper.java
index 33906f8b305..885a8d89908 100644
--- a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/FilesetMetaMapper.java
+++ b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/FilesetMetaMapper.java
@@ -190,28 +190,28 @@ Integer updateFilesetMeta(
   @Update(
       "UPDATE "
           + META_TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE metalake_id = #{metalakeId} AND deleted_at = 0")
   Integer softDeleteFilesetMetasByMetalakeId(@Param("metalakeId") Long metalakeId);
 
   @Update(
       "UPDATE "
           + META_TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE catalog_id = #{catalogId} AND deleted_at = 0")
   Integer softDeleteFilesetMetasByCatalogId(@Param("catalogId") Long catalogId);
 
   @Update(
       "UPDATE "
           + META_TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE schema_id = #{schemaId} AND deleted_at = 0")
   Integer softDeleteFilesetMetasBySchemaId(@Param("schemaId") Long schemaId);
 
   @Update(
       "UPDATE "
           + META_TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE fileset_id = #{filesetId} AND deleted_at = 0")
   Integer softDeleteFilesetMetasByFilesetId(@Param("filesetId") Long filesetId);
 }
diff --git a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/FilesetVersionMapper.java b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/FilesetVersionMapper.java
index b2df6ab43cb..af08416ea09 100644
--- a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/FilesetVersionMapper.java
+++ b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/FilesetVersionMapper.java
@@ -73,28 +73,28 @@ void insertFilesetVersionOnDuplicateKeyUpdate(
   @Update(
       "UPDATE "
           + VERSION_TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE metalake_id = #{metalakeId} AND deleted_at = 0")
   Integer softDeleteFilesetVersionsByMetalakeId(@Param("metalakeId") Long metalakeId);
 
   @Update(
       "UPDATE "
           + VERSION_TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE catalog_id = #{catalogId} AND deleted_at = 0")
   Integer softDeleteFilesetVersionsByCatalogId(@Param("catalogId") Long catalogId);
 
   @Update(
       "UPDATE "
           + VERSION_TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE schema_id = #{schemaId} AND deleted_at = 0")
   Integer softDeleteFilesetVersionsBySchemaId(@Param("schemaId") Long schemaId);
 
   @Update(
       "UPDATE "
           + VERSION_TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE fileset_id = #{filesetId} AND deleted_at = 0")
   Integer softDeleteFilesetVersionsByFilesetId(@Param("filesetId") Long filesetId);
 }
diff --git a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/MetalakeMetaMapper.java b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/MetalakeMetaMapper.java
index 2336a6761a6..d1cb2d1ea73 100644
--- a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/MetalakeMetaMapper.java
+++ b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/MetalakeMetaMapper.java
@@ -122,7 +122,7 @@ Integer updateMetalakeMeta(
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE metalake_id = #{metalakeId} AND deleted_at = 0")
   Integer softDeleteMetalakeMetaByMetalakeId(@Param("metalakeId") Long metalakeId);
 }
diff --git a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/SchemaMetaMapper.java b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/SchemaMetaMapper.java
index 3e8723b053d..009cdcb20e5 100644
--- a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/SchemaMetaMapper.java
+++ b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/SchemaMetaMapper.java
@@ -132,21 +132,21 @@ Integer updateSchemaMeta(
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE schema_id = #{schemaId} AND deleted_at = 0")
   Integer softDeleteSchemaMetasBySchemaId(@Param("schemaId") Long schemaId);
 
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE metalake_id = #{metalakeId} AND deleted_at = 0")
   Integer softDeleteSchemaMetasByMetalakeId(@Param("metalakeId") Long metalakeId);
 
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE catalog_id = #{catalogId} AND deleted_at = 0")
   Integer softDeleteSchemaMetasByCatalogId(@Param("catalogId") Long catalogId);
 }
diff --git a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/TableMetaMapper.java b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/TableMetaMapper.java
index f1de8a51bd5..331847f8cdc 100644
--- a/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/TableMetaMapper.java
+++ b/core/src/main/java/com/datastrato/gravitino/storage/relational/mapper/TableMetaMapper.java
@@ -127,28 +127,28 @@ Integer updateTableMeta(
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE table_id = #{tableId} AND deleted_at = 0")
   Integer softDeleteTableMetasByTableId(@Param("tableId") Long tableId);
 
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE metalake_id = #{metalakeId} AND deleted_at = 0")
   Integer softDeleteTableMetasByMetalakeId(@Param("metalakeId") Long metalakeId);
 
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE catalog_id = #{catalogId} AND deleted_at = 0")
   Integer softDeleteTableMetasByCatalogId(@Param("catalogId") Long catalogId);
 
   @Update(
       "UPDATE "
           + TABLE_NAME
-          + " SET deleted_at = UNIX_TIMESTAMP()"
+          + " SET deleted_at = UNIX_TIMESTAMP(CURRENT_TIMESTAMP(3)) * 1000.0"
           + " WHERE schema_id = #{schemaId} AND deleted_at = 0")
   Integer softDeleteTableMetasBySchemaId(@Param("schemaId") Long schemaId);
 }