Abstract: With the full completion of the BeiDou-3 satellite navigation system, its satellite atomic clocks have gradually entered stable operating states. Performance evaluation of the satellite-borne atomic clocks is crucial to improving its global service performance. This paper established the evaluation index of the frequency characteristics of the satellite atomic clock and the corresponding calculation method. The average frequency fitted hourly is used to reflect the frequency accuracy and frequency drift characteristics of the satellite-borne atomic clock, and considering the error characteristics of different clock bias products, the combined Hadamard deviation is proposed to accurately evaluate the frequency stability of the satellite-borne atomic clock. The accuracy of the clock bias determination and the frequency performance of the satellite clocks were evaluated based on the BeiDou-3 multisatellite precision orbit determination (MPOD) and two-way satellite time and frequency transfer (TWSTFT) clock products. The analysis results have demonstrated that, the random noise level represented by the root mean square (RMS) of hourly fitting residual of the TWSTFT clock bias is 0.2~0.25ns, and the random noise level of the MPOD clock bias is not larger than 0.02ns; the measurement accuracy represented by the RMS of daily fitting residual of the TWSTFT clock bias is 0.35~0.42ns, and of the MPOD is 0.1~0.18ns; the frequency accuracy of the satellite atomic clock is in the order of 10^-12~10^-11; the daily frequency drift of the passive hydrogen maser (PHM) is in the order of 10^-15~10^-16, the 30-day frequency drift of the PHM does not exceed the order of 10^-13, and the daily frequency stability reaches the order of 10^-15, while the rubidium clock frequency generally shows obvious frequency drift, and daily frequency drift reaches the order of 10^-13. The frequency drift characteristics and long-term frequency stability of the BeiDou-3 PHM are overall better than the rubidium clocks.