The CO2 permeability and selectivity of CHA-type zeolite membranes in the separation of a CO2/CH4 mixture gas at high pressure were evaluated using non-equilibrium molecular dynamics (NEMD). It was found that in a perfectly crystalline, defect-free CHA membrane, the adsorption of CH4, which diffuses slowly in the pores, hinders CO2 permeation. Therefore, an increase in the amount of CH4 adsorbed at high pressure decreases the CO2 permeability and significantly reduces the CO2 selectivity of the CHA membrane. CHA membranes with grain boundaries parallel to the permeation direction were found to show higher CO2 selectivity than perfectly crystalline CHA membranes at high pressure, as the blocking effect of CH4 on CO2 permeation occurring within the grain boundary is not significant. This paper is the first to show that the CO2 permeability of CHA membranes with controlled grain boundaries can exceed the intrinsic performance of fully crystalline zeolite membranes at high pressure.