Abstract: A mathematical model for simulating the longitudinal distribution of pH in MFE（Multichannel Flow Electrophoresis) is proposed on the basis of mass transfer analysis of electrophoresis and electrolysis equilibrium of electrolytes.This model was used for selecting suitable operating conditions to establish an expected pH gradient with conventional electrolyte,which is of essential importance in achieving a high resolution in an electrophoresis process conducted in multicompartment electrolyzer.A numerical solution was developed on the basis of Gear method.The calculated results agreed well with the experimental data in a wide range of applied potential and protein concentration in solution.This model may also be applied to other ampholyte-free electrophoresis processes conducted in the multicompartment electrolyzer.