A synchronization system for transform databases and a method thereof are provided. The system includes a database transformer and a data adapter. The database transformer is used to transform tables from a source database to a target database. The data adapter includes a statement parsing unit, a storage unit and a synchronization control unit. The statement parsing unit receives a query statement and parses a query table associated with the query statement. The storage unit stores the query statement temporarily. The synchronization control unit determines a query mechanism and receives a transformation state about the query table from the database transformer. Based on the query mechanism and the transformation state, the synchronization control unit performs the query statement in the source database, the target database, or both of them. |