Natural gas is currently the main industrial source of helium, thus He/CH4 separation has become increasing important, where two-dimensional materials have been considered to be a potential solution, but the gas transport mechanism within nanopores is not yet clear. Here, both non-equilibrium molecular dynamics (NEMD) and equilibrium MD (EMD) were employed to study the transport of He/CH4 through nanopores of different MXenes with various pore diameters (d), nanopores’ density and functional groups, which shows two main transport mechanisms, molecular sieving or Knudsen diffusion. Small d is found to be crucial for the molecular sieving mechanism and consequently, high He/CH4 selectivity (SHe/CH4). The density profiles of He/CH4 along permeation direction from EMD simulations were used to predict SHe/CH4 and permeance for the gas passing through different nanopores, yielding results well agreeing with NEMD simulations. This work provides theoretical insights into gas transport in MXene nanopore for future nanopore designing engineering.