The invention provides a heterogeneous database synchronization method and an application system. A synchronous processor arranged on a side of a source data source can periodically poll change data recorded in a synchronous change table and encapsulate the change data into a data stream to send the data stream to a synchronous analyzer arranged on the side of a target database. The synchronous analyzer de-capsulates the data stream, then maps the change data in the source data table into a data structure of a target data table in the target database according to preset mapping files, and synchronizes the data of the target data table according to the change type values in the change data so as to complete the data synchronization of heterogeneous databases. The heterogeneous database synchronization method and the application system disclosed by the invention can achieve the data synchronization of heterogeneous databases just by setting different mapping files on the synchronous analyzer instead of changing the existing heterogeneous databases, the implementation is simple, and the expansion is easy.