Measurement noise of atomic clocks influences the evaluation of frequency stability, especially for the short term and medium term frequency stability. Overlapping Allan variance can overcome in-stability due to FFM and RWFM noise variety along with time, but the result is influenced by measure noise. The method of evaluating frequency stability for atomic clocks is given basing on mathematic model and noise characteristic of atomic clocks. A processing method using smoothing window is presented. The noise of time difference sequence is restrained through adding window and smoothing. A experiment is executed with time difference sequence of rubidium clock, and the result shows that the reliability of short term stability(100~1 000)s can be improved by 100 points smoothing method.