Abstract: Joule heating in the microchannel of CE microchip was simulated and analyzed by CoventorWare microfluidic software.BSA and Lys were selected as the samples for detection.The effects of joule heating on the separation efficiency were investigated by adjusting insulator layer thickness,separation field strength,buffer concentration,etc.The results showed that it was essential to decreasing Joule heating by suitable ways in the electrophoresis separation process on microchip.