Computer simulations have been performed to study the effects of surface heterogeneity on gas permeation through slit-like carbon membranes by using a novel simulation technique, mu VT ensemble Non-Equilibrium Molecular Dynamics. The energetically heterogeneous surfaces are made by randomly removing a certain number of carbons on the first layer of graphite basal planes. Methane (1) and ethane (2) are used as model gases for pure- and mixed-gas permeations. A small heterogeneity on the pore surface is found to result in a large decrease in the permeation fluxes due to an increase in frequency of molecular collisions onto heterogeneous sites. The densities in equilibrium with feed gases decrease almost linearly with an increase in the surface heterogeneity, though the decrease is not so large as that in permeation fluxes. In the case of the permeation of a binary mixture, permselectivity of a more adsorptive substance (ethane), which is much larger than the ratio of pure gas permeances, (P) over cap 2/(P) over cap 1, is found to change only slightly with an increase in the surface heterogeneity.