In order to avoid introducing periodic fluctuations in the clock offset of onboard atomic clock into the system time, it is necessary to eliminate the periodic fluctuations when establishing the autonomous time benchmark of satellite navigation system constellation. Based on the clock offset of BeiDou atomic clock provided by IGS, a method of periodic fluctuation correction for onboard atomic clock based on spectrum analysis was proposed. By comparing the performance of frequency stability of onboard atomic clock offset before and after correction, it is proved that this method can successfully eliminate the periodic fluctuation of satellite clock offset caused by environmental factors. Performances of different types of onboard atomic clock of BeiDou are improved after correction. Through this method, performances of onboard atomic clocks with different orbital types in the system have been improved remarkably. Among them, the frequency stability in 10 000 seconds of GEO(geostationary satellite) satellite-borne atomic clocks has been improved about 50%, MEO(medium orbit earth satellite) about 23%, and IGSO(inclined geosynchronous orbit satellite) about 15%. Through this correction method, the frequency stability of cesium clocks in ground stations has been achieved in both BDS-2 and BDS-3 satellite-borne atomic clocks, which lays foundation to the star autonomous timekeeping based entirely on satellite-borne atomic clocks.