Comparing and analysis on the satellite clocks basic characteristics, frequency stability, and clock offset prediction accuracy of three types of BDS On-orbit Satellite Clocks, including RAFS-1, RAFS-2, and PHM. The results show that the performance index of the PHM clocks is significantly better than the RAFS. The performance index of the RAFS-2 clocks is significantly better than the RAFS-1, and the frequency stability and clock offset prediction accuracy is improved by about one times. Additionally, the RAFS-2 clocks adds the phase connection function, which can protect the satellite clock provide a continuous phase.