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Natural gas dehydration is a critical process in natural gas extraction and transportation, and the membrane separation method is the most suitable technology for gas dehydration. In this paper, based on molecular dynamics theory, we investigate the performance of a metal–organic composite membrane (ZIF-90 membrane) in natural gas dehydration. The paper elucidates the adsorption, diffusion, permeation, and separation mechanisms of water and methane with the ZIF-90 membrane, and clarifies the influence of temperature on gas separation. The results show that (1) the diffusion energy barrier and pore size are the primary factors in achieving the separation of water and methane. The diffusion energy barriers for the two molecules (CH₄ and H₂O) are ΔE(CH₄) = 155.5 meV and ΔE(H₂O) = 50.1 meV, respectively. (2) The ZIF-90 is more selective of H₂O, which is mainly due to the strong interaction between the H₂O molecule and the polar functional groups (such as aldehyde groups) within the ZIF-90. (3) A higher temperature accelerates the gas separation process. The higher the temperature is, the faster the separation process is. (4) The pore radius is identified as the intrinsic mechanism enabling the separation of water and methane in ZIF-90 membranes.