Abstract: We established the channel model of microfluidic chip and simulated the flow field by CFD in order to research the bad peak repetition during continuous electrophoresis analysis on microfluidic chip.It was indicated by the CFD simulation that the sample dilution by buffer which was pushed into the sample reservoir by the flow field during separation caused the bad peak repetition.The results of experiments proved the result of simulation.Furthermore we optimized the separation parameter and successfully decreased the peak RSD from 20%-30% to less than 10% which greatly increased the repetition and stability of continuous electrophoresis analysis.