In this study, novel polysulfone-based cation-exchange membranes with strong mechanical strength have been developed and applied in ion-exchange-membrane-partitioned free-flow IEF (IEM-FFIEF) to replace the conventional immobiline membranes. A fundamental understanding of protein mass transfer in the IEM-FFIEF process has been revealed experimentally with the aid of membrane-based boundary effect model contributed by Ennis et al. we have proven experimentally the existence of a pH gradient across the membrane cross-section when an IEM-FFIEF system is in operation. The boundary effects on particle velocities are calculated based on the IEF assumption and various characterizations, and are compared with the experimental results. In the IEM-FFIEF experiments, a protein mixture (BSA and myoglobin (Mb)) and sulfonated polysulfone membranes with different ion-exchange capacities are applied. Experimental results show that the real velocity and real mobility (of Mb in this study) are comparable with the mathematic model developed by Ennis et al. This suggests that the equation proposed by Ennis et al., is sufficient to capture the mass transfer through membrane in the IEM-FFIEF system after considering the effects of pore size distribution and effects of disturbed electric field. The charge properties of the membrane surface play a dominant role on the separation performance of the membranes. The newly developed porous solid-phase ion-exchange membranes may potentially and effectively replace immobilines to perform the selective function for protein separation.