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The BeiDou Navigation System has currently no sufficient ground stations to support continuous monitoring frequency data of the atomic clocks contained in the MEO satellites.As a result,the obtained frequency data of MEO satellite clocks are discontinuous,which makes it difficult to estimate the frequency stability of the clocks.To overcome the difficulty,a method of calculation using discontinuous frequency data to estimate frequency stability of an atomic clock is presented in this paper.The calculation can be divided to three steps.Firstly,the discontinuous frequency data are fitted with a polynomial function,and the residuals are obtained after removal of the systematic deviation.Secondly,the discontinuous residuals are linked up to form a new groupof continuous residuals,and based on which frequency stability is calculated.Finally,the obtained long-term frequency stability is modified by using bias function developed by Barnes.The method has been tested on a set of frequency data,with length of 4 months,of a rubidium atomic clock.The Allan variance stabilities obtained by the method are in good agreement with those of the calculation based on the original data,which implies that the method is basically feasible.