• Montmorillonite, kerogen and MMT-kerogen composite slit nanopores with desirable pore sizes are constructed; • GCMC and EMD simulations are conducted to study the sorption and self-diffusion behaviors of methane in various nanopores; • Pore surface roughness can impede the diffusion of gases, especially in smaller pores. Up to now, a large number of studies have utilized various representative materials to approximate the replacement of shale and investigate the gas adsorption and diffusion behavior in various shapes of nanopores by means of molecular simulations. However, the study of methane sorption and self-diffusion behavior under high temperature and pressure reservoir conditions in deep shale is not clear. In this study, we first established montmorillonite (MMT), kerogen and MMT-kerogen composite slit nanopores using representative shale components of MMT and kerogen. On this basis, we investigated the methane sorption and self-diffusion characteristics employing the grand canonical Monte Carlo (GCMC) and equilibrium molecular dynamics (EMD) simulations. The results show that the differences in the molecular composition and structure of MMT and kerogen surfaces lead to stronger adsorption performance of MMT surface than kerogen in a single nanopore for the same conditions, which results in the inhomogeneity of spatial distribution of methane molecules in the pores. While the sorption capacity of the kerogen matrix is more potent than MMT due to its larger specific surface area (SSA). The smaller pores have stronger adsorption capacity compared to the larger pores. At the same time, the methane density profiles indicate that the adsorption of the MMT and kerogen in smaller pores is less differentiated. The methane sorption energy distribution and isosteric heat of sorption also mutually corroborate the more stable methane sorption at a higher pressure and smaller pores. The self-diffusion coefficient of methane in nanopores gradually decreases with increasing pressure, with a more pronounced variation at lower pressure. Pore surface roughness will hinder the diffusion of gas, and the closer the distance is, the more noticeable the effect will be. This study sheds light on the sorption and self-diffusion phenomena and difference of gas in monospecific and composite nanopores, which provides insights into the reserve evaluation and development of the deep shale gas reservoirs, and is further expected to furnish ideas for exploring the occurrence and transport characteristics of supercritical fluids on other composite nanomaterials.