Carbon molecular sieve membrane (CMSM) is the promising candidate for natural gas purification because of its excellent stability, per-selectivity and permeability. However, morphological design of CMSM is very important for the specific application. In this project, two CMSM samples were synthesized at different pyrolytic conditions and examined for separation of N2/CH4 gas pair. Adsorption and permeation experiments were conducted to examine the separation performance of each membrane sample. At the ambient conditions, a perm-selectivity of ~ 6 was found for (N2/CH4) pair while it is ~30 for (CO2/N2) pair on the membrane pyrolyzed at the lower pyrolytic temperature of 800°C. When pyrolytic temperature is increased to 1000°C, however, these two selectivity values are changed to ~1.5 (decrease) and ~ 100 (increase), respectively. Analysis revealed that both surface diffusion and molecular sieving play important roles in the overall gas permeation mechanisms, which result in the abnormal behaviors in the selectivities of different gas molecules. It is concluded that the variation of pore size and thickness are critical for the design of surface flow selective carbon molecular sieve membranes.