Abstract: Shale gas is a hot spot of research in unconventional oil and gas. Strengthening the study of methane percolation mechanism is of great significance to the development of shale gas reservoirs. By simulating the flow behavior of methane molecules in nanopores based on molecular dynamics, this paper establishes a pore model of slits; on this basis, it further analyzes the influence of pore size, pressure, mineral species and pore water content on the diffusion capacity of methane molecules, and explores the diffusion law of gas in microscopic porous media. The study shows that the diffusion of methane molecules accelerates when the temperature and pore size increase, while becomes slower when the pressure increases. The types of minerals on the pore walls have a significant effect on the diffusion of methane molecules, and the diffusion coefficients in organic matter, quartz and kaolinite decrease sequentially. The organic pores in graphene have greater adsorption capacity for methane than inorganic pores. It is mainly because the unique structure and smooth surface of graphene promote the diffusion of methane molecules. Water molecules inhibit the diffusion of methane molecules. The diffusion coefficient of methane gradually decreases with the increasing of water content. The water molecules in organic pores hinder the diffusion of methane molecules in the form of clusters, while the water molecules in inorganic pores are adsorbed on the pore wall surface in the form of "water film". When the water content in the pores of inorganic minerals is too high (ρ_w≥50 % ), the water molecules in pores will gather to form "water bridge", resulting in the diffusion coefficient of methane in the inorganic pores being lower than that in the organic pores.