The mu VT-NEMD method, a combination of the mu VT-MC and the boundary-driven NEMD, is used for simulating permeation of pure and mixed gases through slit-shaped carbon membranes with belt-like heterogeneous surfaces under the assumption of local adsorption equilibrium at the membrane entrance. The belt-like heterogeneous surfaces are made by removing carbon atoms of the first layer in a lint vertically to the permeate direction. Methane and ethane are used as permeating gases. The values of permeation resistance increase almost exponentially with an increase in the potential barrier; the resistance for ethane is always larger than that for methane. In the case of a binary system, the permselectivity is determined by the adsorption equilibrium at the feed side when the potential barrier is low, while it sharply decreases with increasing potential barrier. This result suggests that the separation mechanism changes from the adsorption equilibrium control to the permeation rate control in the pore. The curve of the molar flux of ethane against temperature has a minimum point where temperature is about 510 K.