Evaluating and analyzing the performance of GNSS on-board atomic clock is a significant means to know the operational condition of satellite clocks, which plays an important role in fields of integrity monitoring, performance evaluation, satellite clock bias (SCB) determination and prediction of the satellite navigation system. The beidou satellite navigation system (BDS) is composed of satellite types with different functions and orbital altitudes, leading to the presence of some new features of the atomic clock in its constellation, which is different from other navigation systems. The existing BDS satellite-borne atomic clock performance evaluation has less detailed attention to the relevant characteristics of the evaluation data itself, and the performance analysis of the long time period is still relatively limited. Aiming at the discussion above, the paper firstly analyzes the characteristics of the SCB data derived from multi-satellite orbit determination in a long time, and then uses the frequency stability which is used as an index to reflect the of the performance of a high precision atomic clock to evaluate and analyze the characteristics of BDS satellite clock in detail. At the same time, the data preprocessing strategy and frequency stability calculation strategy are designed to calculate the frequency stability. Finally, some conclusions are obtained as follows: (1) there is a certain amount of abnormal value in the SCB data derived from multi-satellite orbit determination during the long continuous operation of BDS satellite clocks, and appropriately preprocessing data is very necessary; (2) the proposed data preprocessing method and frequency stability calculation strategy is effective; based on daily SCB data to calculate the frequency stability, the long-term change of the calculated sequence is relatively stable, and the frequency stability for averaging time of 1 hours and 2 hours is all basic in 10 -14 orders of magnitude; based on SCB data from one year, the mean value of the frequency stability for averaging time of 2 hours, 6 hours and 12 hours and 24 hours are 6.5x10-14 (±2.1x10-15 ), 7.4x10-14 (±4.5x10-15), 7.1x10-14 (±5.7x10-15 ) and 4.4x10-14 (±4.1x10-15 ), which are calculated according to the sampling interval of 15 days; (3) MEO spaceborne atomic clocks have the best frequency stability, followed by IGSO satellites, and GEO satellite clocks is relatively worst; the daily stability of BDS spaceborne atomic clocks remains at the level of 2.0~8.0x10-14 .