Using molecular dynamics, we simulated the diffusion behavior of supercritical methane in shale nanopores composed of different matrix mineral types (organic matter, clay, and calcite). We studied the effects of pore size, pore pressure, and moisture content on the diffusion process. Our results show that confined methane molecules diffuse more rapidly with increases in pore size and temperature but diffuse slowly with an increase in pressure. Anisotropic diffusion behavior is also observed in directions parallel and perpendicular to the basal surfaces of nanoslits. We also found that mineral types composing the pore walls have a prominent effect on gas diffusion. The perfectly ordered structure and ultrasmooth surface of organic matter facilitate the transport of methane in dry pores, even though its adsorption capability is much stronger than that of inorganic minerals. Moisture inhibits methane diffusion, but this adverse effect is more evident in organic pores because water migrates in the form of cluster, which acts as a piston and severely impedes methane diffusion. However, only an adsorbed water membrane is present at the surfaces of inorganic materials, leading to a weaker impact on methane diffusion. Remarkably, the ratios of the self-diffusion coefficients of the confined fluid and bulk phases at different temperatures collapse onto a master curve dependent solely on the slit aperture. Therefore, we propose a mathematical model to facilitate up-scaling studies from atomistic computations to macroscale measurements. The findings of this study provides a better understanding of hydrocarbon transport through shale formation, which is fundamentally important for reliably predicting production performance and optimizing hydraulic-fracturing design.