Abstract: The molecular simulation method was introduced in the context of membrane filtration process of biomolecules to investigate the effect of monomer structure on its charge property, and also the interaction between membrane and biomolecules, thus providing theoretical information on the selection of monomers in membrane charge modification.Amino acids and dipeptides were taken as samples in the simulation process. Hyperchem software was used to investigate membrane modification by acrylic acid, quaternary ammonium compound and their derivatives, and the appropriate operation conditions in microfiltration process of biomolecules.The experimental work on membrane charge modification confirmed the simulation results. Interaction energy results also proved to be in agreement with previous experimental work. The present study illustrated that the molecular simulation method could be of practical importance in the design of separation material and optimization of separation process.