Time synchronization error sources of the GPS/SINS integrated navigation system in high dynamic environment were magnified to different degrees. As a result, the integration capability of the system was badly affected consequently. A thought of designing the synchronized time benchmark and recording the communication delay of the GPS in the hardware was presented. Based on it, the time mark difference between the two subsytem, the drift of the SINS' frequency mark and the communication delay were considered as the synchronization error sources of the system. In order to synchronize the measurements at every synchronization point, the modeling of the drift, the extrapolated calculation of the measurements and the filtering compensation for the communication delay were accomplished using the software processing methods. Simulation results show the efficiency of the method.