We have realized a time synchronization system using the one pulse per second (1PPS) signal provided by the global navigation satellite system (GNSS) receiver as reference signal to synchronize the 1PPS signal output of the local oscillator. Aiming at the influence of the jitter noise of GNSS receiver 1PPS signal on synchronization performance of the time synchronization system, we designed a filter that can suppress the jitter effect. The filter adopted the manner of wavelet filter combining with moving average filter, in which the wavelet filter used customdefined threshold and threshold functions. Filtering processing experiment was conducted using the designed filter, the experiment results reveal that the jitter noise suppression effect for the 1PPS signal of the GNSS receiver using the proposed filtering scheme is better than that using commonly used Kalman filter. The 1PPS output signal accuracy of the proposed time synchronous system reaches 117 ns, which is one order superior to the 1PPS signal accuracy of GNSS receiver.