Abstract The atomic clocks onboard navigation satellites provide the reference frequency for the navigation signals, and the stability of the clock will directly influence the accuracy of timing and positioning performance. In this paper, the IGS MEGX clock products for Beidou satellites are used for analysis,and the Hadamard variance is used to calibrate the clock stability of all orbiting Beidou satellites. The results show that the clocks onboard Beidou satellites are relatively stable over 1 year’s analysis; and the Hadamard variance is about 10-13 on 300 s interval with slight differences between different Beidou satellites. Compared with GPS satellite clocks, the stability performance is between those of GPS ⅡR-M and GPS ⅡF satellite clock performance. These results are beneficial for navigation and positioning users.