The water control mechanism of relative permeability modifier (RPM) are studied with molecular simulation technology and core flow apparatus for further study at molecular level, and then building the dynamic model of oil(n-hexadecane)/water mixed phase passing the RPM-laden SiO2 surface. The model shows that the RPM has swelling state in water phase, but contracting in oil(n-hexadecane) phase. The ratio of oil(n-hexadecane)/water mixed phase diffusion coefficient is 4.2, it is equal to the experimental data based on core flow apparatus. The water control mechanism of relative permeability modifier(RPM) can be explained by swelling-contracting mechanism and oil-water fluid partitioning mechanism.