We designed a series of porous graphene as the separation membrane of H₂/N₂. The selectivity and permeability could be controlled by drilling various nanopores with different shapes and sizes. The mechanisms of hydrogen and nitrogen to permeate through the porous graphene are different. The small nanopore (pore-11) can only allow the hydrogen molecules to permeate due to the size restriction. In the systems of bigger nanopores (e.g., pore-13, pore-14, etc.), where the pore size is big enough to allow nitrogen molecules to permeate without any restriction, we observed more permeation events of nitrogen than that of hydrogen molecules. The reason is that the van der Waals interactions with the graphene membrane make the nitrogen molecules accumulate on the surface of graphene. When the pore size further increases, the flow of hydrogen molecules exhibits the linear dependence on the pore area, while there is no obvious correlation between the flow of nitrogen molecules and the pore area.