We present that the porous two-layer membranes of graphene and hexagonal boron nitride (h-BN) are promising for gas mixture separation. For the two-layer membranes, the mechanisms of the gas separation are (i) the different adsorption properties of gases on two membranes inducing a permeation flux difference from one side to the other and (ii) the asymmetric potential energy curves (potential energy of a gas molecule vs distance between the pore center and a gas molecule) of a two-layer membrane leading to a potential energy difference, which can affect gas permeation through the pore. As a concrete example, we explore the gas separation of CO2 and CH4 by the two-layer membrane using molecular dynamics simulations. Finally, on the basis of the distinctive permeation rates in the two directions, a gas separation system with two back-to-back arrayed graphene/h-BN membranes with big pores is designed to realize gas separation.