Basic knowledge regarding flow at conventional scales is relatively familiar to us. However, micro-scale flow is distinctly different. To explore the flow characteristics and mass transfer process in a membrane micro pore, a Knudsen-molecular diffusion mechanism with sliding boundary condition is used to simulate the treatment of ethyl acetate solution using vacuum membrane distillation. The diffusion coefficient is expressed by the Knudsen diffusion coefficient and molecular diffusion coefficient. The simulation results are consistent with the experimental data. The flow fields in the membrane pore are obtained, and the effects of the membrane structure parameters on the membrane pore separation performance are investigated. The results show that the increase in the porosity and pore diameter can enhance the membrane flux and increase the tortuosity and pore length against permeate flux. The optimal choice of the separation factors is presented as a function of the increase in the porosity, pore diameter, and tortuosity. Pore length does not enhance the membrane separation performance. The simulation of the phenomenon occurring in membrane pores should contribute to appropriate membrane preparation and improve membrane separation performance.