Abstract: In GNSS high-precision applications, transmit satellite clock stability is one of the core fac-tors which can directly affect the data processing performance. In this paper, the short-term stabilities of GNSS clocks are investigated with 20 Hz dual-frequency ground-based observations. In date processing procedure, the receiver clock bias are removed with single difference between two satellites, and the night-time dual-frequency observations were used to form the ionosphere-free measurements to avoid the ionosphere delays. Thus, the troposphere delays are corrected with empirical model and mapping function for residual delays. The satellite clock bias are identified by Lag1 autocorrelation function, and the short-term stability of different GNSS satellite atomic clocks are analyzed with Allan deviation. The results show that the single-difference clock stability of GPS, GLONASS and BeiDou are almost on the same magnitude, which is about 10^-10 degree on 0.05 second interval and 10^-11 degree on 1 second interval. Thus, the single-different strategy can be validated for BeiDou radio occultation data processing.