Abstract: As one of the typical microfluidic device,microchip electrophoresis is of the low Reynolds number,low volume flow-rate.Electro-osmosis is the very important physical phenomenon,and its magnitude of the numerical value will affect the precision and veracity of the separation and analysis result.Based on the theory of low Reynolds number,electro-osmosis mathematics model in the micro-channel of microchip electrophoresis is set up,and solved with finite difference method.While the Debye length is 5 nm,with different Zeta potential,the electro-osmosis flow in the micro-channel is plug-like.And the maximal velocity of the electro-osmosis flow rate increase linearly with the Zeta potential increases.While the Zeta potential is-100mV,the electro-osmosis potential in the normal direction decreases exponentially with different Debye length.The distribution of the electro-osmosis flow velocity is almost the same with different Debye length.And the maximal velocity of the electro-osmosis flow would not change when the Debye length changed.