Pore density and pore size are two factors for gas molecular permeation and separation in nanoporous membranes. The nanopores on the membranes can be tuned to control gas molecular permeation and separation. But how the pore density can influence the permeation and how the pore size of multilayer nanoporous membrane can be tuning to influence the selectivity have not been fully addressed from a computational simulation. Here we use molecular dynamics (MD) simulation to investigate gas molecular permeation and adsorption behaviors by changing the pore densities of a nanoporous graphene membrane from 0.01 nm-2 to 1.28 nm-2 and adjusting the effective pore size by tuning the offset of bilayer graphene membrane. We find that the higher pore density leads to higher permeation for both CO2 and He, but the increase rate slows down only for CO2. And We also find that offset can influence the effective pore size, which can be used to build bilayer gas separation membrane flexibly.