Abstract: On-board atomic clock as the key to maintain the time scale, its performance will affect the navigation, positioning and timing of the user's accuracy. The definition and calculation method of atomic clock frequency accuracy, drift and stability were introduced, using satellite clock error data provided by iGMAS, IGS and MGEX in the GNSS on-board atomic clocks performance assessment. And, on this basis we analyzed the characteristics of GNSS on-board atomic clocks. The results show that the rubidium clocks on GPS BLOCK IIF and the space borne hydrogen clocks in Galileo system have the best comprehensive performance; the day stability of BDS MEO and IGSO on-board atomic clocks have reached the level of 2~4×10^-14, almost the same precision as the GPS BLOCK IIR satellites; and the frequency accuracy reached the level of 1~4×10^-11, and the frequency drift reached the level of 10^-14.