Membrane distillation technology, as a new membrane-based water treatment technology that combines the membrane technology and evaporation process, has the advantages of using low-grade heat, working at atmospheric pressure with simple configuration, etc. In this study, heat and mass transfer were coupled at the membrane surfaces through the user-defined function program. The effects of feed temperature, feed velocity and permeate velocity on temperature polarization were mainly investigated for a high-concentration NaCl solution. The temperature polarization was increased with the increase of feed temperature and the decrease of feed and permeate velocity. The effects of temperature, inlet velocity and solution concentration on the evaporation efficiency of the membrane module for co- and counter-current operations were investigated in detail. The counter-current operation performed better than co-current operation in most cases, except for the condition where the NaCl concentration was relatively low or the module length was long enough. In addition, the optimal membrane thickness for both PVDF and PTFE was studied. The optimal membrane thickness was found in the range of 10 to 20 μm, which corresponded to the highest permeate flux for the selected materials, pore size distribution, and operation conditions. Membrane material with lower thermal conductivity and larger porosity was prone to get higher permeate flux and had larger optimal membrane thickness. Increasing feed velocity or feed temperature could decrease the optimal membrane thickness.