Clarifying the mechanism for the gas transportation in the emerging 2D materials-based membranes plays an important role on the design and performance optimization. In this work, the corresponding studies were conducted experimentally and theoretically. To this end, we measured the gas permeances of hydrogen and nitrogen from their mixture through the supported MXene lamellar membrane. Knudsen diffusion and molecular sieving through straight and tortuous nanochannels were proposed to elucidate the gas transport mechanism. The average pore diameter of 5.05 Å in straight nanochannels was calculated by linear regression in the Knudsen diffusion model. The activation energy for H2 transport in molecular sieving model was calculated to be 20.54 kJ mol−1. From the model, we can predict that the gas permeance of hydrogen (with smaller kinetic diameter) is contributed from both Knudsen diffusion and molecular sieving mechanism, but the permeance of larger molecular gases like nitrogen is sourced from Knudsen diffusion. The effects of the critical conditions such as temperature, the diffusion pore diameter of structural defects, and the thickness of the prepared MXene lamellar membrane on hydrogen and nitrogen permeance were also investigated to understand the hydrogen permeation difference from Knudsen diffusion and molecular sieving. At room temperature, the total hydrogen permeance was contributed 18% by Knudsen diffusion and 82% by molecular sieving. The modeling results indicate that molecular sieving plays a dominant role in controlling gas selectivity.