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• Simulate He/CH 4 passing MXene nanopores with NEMD, Non-Equilibrium Molecular Dynamics. • MXene nanopores exhibit excellent P He (permeance) & S He/CH4 , even for He/CH 4 mixture. • Gas passes through nanopores with various mechanisms, depending on the pore diameter. • Applied transition state theory to predict S He/CH4 (selectivity) for small nanopores. • Relate density profiles of Equilibrium Molecular Dynamics simulations to P from NEMD. Natural gas is currently the main industrial source of helium, thus He/CH 4 separation has become increasing important. Nanopores based on two-dimensional materials have been considered as very promising for He/CH 4 separation, but the transport mechanism through them is yet unclear. Here, both non-equilibrium molecular dynamics (NEMD) and equilibrium MD (EMD) were employed to study the transport of He/CH 4 through nanopores of different MXenes with various pore diameters (d), pore density and functional groups, which showed two main transport mechanisms, molecular sieving and Knudsen diffusion. Small d was found to be crucial for the molecular sieving and consequently, high He/CH 4 selectivity (S He/CH4). The density profiles of gas molecules in EMD simulations were used to predict S He/CH4 and the permeance for gas passing through different nanopores, yielding results well agreeing with NEMD simulations. This work provides theoretical insights for gas transport through MXene nanopore and may help designing nanopores in the future. [ABSTRACT FROM AUTHOR]