Abstract: In the satellite navigation system, the atomic clock is the time measurement benchmark and the core component. Its performance directly determines the quality of navigation, positioning and time service. The performance evaluation of in-orbit atomic clock is the precondition and foundation to ensure the normal operation of satellite navigation system, and also has important reference value for the improvement of atomic clock product performance. The main parameters and evaluation methods of atomic clock performance evaluation are introduced. The clock difference data between Beidou and GPS atomic clocks is analyzed and compared. The results show that the accuracy, stability and drift rate of the Beidou-2 rubidium atomic clock are different from those of the GPS atomic clock. Beidou-3 is equipped with rubidium atomic clocks and hydrogen atomic clocks, and its performance indicators have been greatly improved. The 10 days stability and daily stability of hydrogen atomic clocks have generally reached the 10⁻¹⁵ level, and their performance indicators are equivalent to GPS. The long-term frequency stability of the rubidium atomic clock carried by the latest GPS Block IIF satellite has been significantly improved, and the performance indicators of the domestic rubidium atomic clock need to be further improved.