Abstract: In order to have a good understanding of the characteristic of time-domain frequency stability for the atomic clock,the effects of the main error sources on the time-domain frequency stability were studied,including measurement resolution uncertainty,phase steps and frequency spikes,leakage errors and end-of-data,and so on.The approximate formulas for the effects of the main error sources are deduced.The characteristics of the effects are also analyzed.Then the corresponding methods for reducing the error sources are given.The validity of the methods is verified using simulated data.