With the rapid development of micro-electromechanical system, micro fluidic controlling system has become the key problem in present and future study in research fields. To eliminate the pulsation component and to study the effect of various factors on flow stability play a crucial role. Based on numerical analysis, the process of periodic flow was calculated, the influences of the average speed of periods, vibration amplitude of fluctuating velocity, pulsation frequency on filtering efficiency were analyzed. The results show that the filtering efficiency of the first level filtering cavity is affected by the average speed of periods; filtering efficiency become lower with the average speed of periods increased; compare with the first level, the second and the third level filtering cavitys filtering efficiency are less affected by the influence factors and these can be ignored.