The time system adopted by the four major satellite navigation systems is introduced, the research content and research method of frequency standard time domain frequency stability are analyzed, and its practical calculation method and formula are deduced. The frequency stability of the satellite-borne atomic clocks of various navigation systems is compared and analyzed. The comprehensive data shows that most of the space-borne clocks can reach the order of 10-14. Among them, the GPS space-borne rubidium clock and Galileo The on-board PHM clock has the best stability.