In allusion to the database server of tree distribution in the network environment, this paper proposes a heterogeneous database synchronization mechanism based on the shadow table method. In this paper, the application environment of the isolation netgap is described, and the overall architecture of the synchronization system is introduced, and the implementation of the module such as change data capture, incremental file generation, data synchronization operation and exception handling is proposed. Finally, the database synchronization mechanism is verified by the application of the data acquisition system of an organization.