Abstract: A method to improve the long-term stability of crystal oscillator is studied in this paper. The 1 pulse per second signal (1 pps) from GPS/BDS receiver is used as the reference signal to correct and compensate the frequency offset of crystal oscillator, to obtain better long-term stability without destroying the short-term stability of crystal oscillator. Median average filter and Kalman filter are mainly used to eliminate the jump and random jitter of phase. Based on this value, the incremental PID algorithm with dead zone is used to control the crystal oscillator frequency to synchronize with GPS/BDS signal. The test results show that the peak-to-peak value between the crystal oscillator and cesium clock is less than 47 ns, the Allan variance of 100 second sampling is 6.22×10⁻¹¹, and the Allan variance of 10 000 second sampling is about 1.02×10⁻¹². It is proved that this method can help the crystal oscillator obtain better long-term stability, it is a reliable method.