Abstract: Space-borne atomic clocks act as satellite time reference in satellite navigation systems, and their performance directly determines navigation and positioning accuracy. The Chinese BeiDou satellite navigation system (BDS) is in full construction phase Thus, it is very important to evaluate the performance of the system. Combining the calculated results of the Hadamard Variance, the Overlapping Hadamard Variance, and the Hadamard Total Variance, currently available for evaluating the stability of space-borne rubidium atomic clocks, this paper comprehensively evaluates the frequency stability of BDS satellite clocks by using precise satellite clock bias data with 5-min and 15-min sampling intervals. Meaningful conclusions are drawn.