The demand on energy is rising and shale gas as an important unconventional energy resource has received worldwide attention. It has shown a significant effect on the world's energy structure after the commercial exploitation of shale gas in the United States. Understanding diffusion and permeation of shale gas at geological depths is quite essential, but it cannot be described by traditional Fick or Knudsen diffusion models. In this work, we use dual control volume-grand canonical molecular dynamics method to systematically investigate the permeation process of shale gas in montmorillonite (i.e., a clay mineral of shale) at different geological depths. Results indicate that temperature, pressure, and pore size have an important effect on the permeability, and Knudsen equation cannot describe the permeability of shale gas. Accordingly, on the basis of these simulated data, we propose a new mesoscale model to describe the permeability of shale gas at geological depths. The new mesoscale model shows extensive applicability and can excellently reproduce the extrapolation testing data, and it satisfactorily bridges the gap between Knudsen diffusion and Fick diffusion, which provides important fundamentals for exploitation of shale gas. (C) 2017 American Institute of Chemical Engineers