Abstract: Application of computational fluid dynamics (CFD) to multichannel flow electrophoresis (MFE), a preparative electrophoresis process performed in a membrane spaced multicompartment electrolyzer, was attempted in order to simulate fluid flow in each compartment, which was fundamental in MFE process optimization and apparatus design. A mathematical model describing the distribution of pH and buffering ions along the flow direction in each compartment was established on the basis of mass transfer analysis and electrolysis equilibrium, as well as electric neutrality. The validity of the model was demonstrated by good agreement between the calculated data and the experimental results. The establishment of this model paves the way for the subsequent study of CFD simulation of MFE.