After officially announced the service of BDS-3 system, the promotion and industrial application of BDS-3 is a new highland for BeiDou innovation and development. Satellites' performances are one of prerequisite for high-accuracy and high-reliability location-based services, in which the atomic clock is playing an important role as the main technology advantage. In order to evaluate the reliability of GNSS and BDS-3 on-orbit atomic clock, this paper compared and analyzed the main technical indicators of the on-board atomic clock based on the GNSS satellite product sequence accumulated by iGMAS Analysis Center. Firstly, using GNSS and BDS-3 satellite clock offset products of 5 years and 2 years respectively, the clock offset performance of each system is analyzed from the aspects of phase, frequency, frequency drift and fitting residuals. Then, the overlapping Hadamard variance is used to evaluate the stability of the atomic clocks. The results indicate that: 1) the continuities of GPS, GLONASS, Galileo and BDS-2 on-board are poor during 2015-2017, in which the phase jumps are relatively obvious. After 2008, the qualities of phase data are improved with fewer modulation operations. Meanwhile, BDS-3 presents a better continuous and high-quality clock for 2019-2020 with less phase-modulation operation. 2) the frequency drift values of GPS, GLONASS, Galileo and BDS-3 satellite clocks are all in the order of 10-19, while the frequency drift values of BDS-2 satellite clocks are in the order of 10-18. In terms of the overall variation trend, the frequency drift of GPS, GLONASS and BDS-2 systems is relatively stable, while the frequency drift of Galileo and BDS-3 systems presents an obvious segmentation phenomenon. The frequency drift of satellite clock of BDS-3 system will increase by one order in 2020 compared with that of 2019, reaching the order of 10(-20). 3) the RMS of fitting clock models for GPS, GLONASS, Galileo, BDS-2 (GEO/IGSO/MEO) and BDS-3 are 0.62 ns, 0.72 ns, 0.99 ns, 1.97/1.61/1.45 ns and 0.85 ns, respectively. 4) The stability of GPS, GLONASS and BDS-2 atomic clocks is maintained at the same order of magnitude, namely 10(-13) and 10(-14) for integration time of 1000 s and 10000 s, respectively. Some of the Galileo and BDS-3 satellites are equipped with high-precision hydrogen clocks, both of which have stability in the integration time of 10000 s with order of 10(-14).