Abstract: The accurate evaluation of shale gas reserves relies on the understanding of methane occurrence characteristics in deep shale reservoirs under high-temperature and high-pressure conditions. First, molecular models of kerogen nanopores with different shapes and sizes were constructed based on kerogen structure unit of deep shale from the Longmaxi Formation. Second, simulations of methane occurrence were conducted by coupling a grand canonical Monte Carlo algorithm and a molecular dynamics algorithm. These simulations were focused on analyzing the influence of pressure, temperature, pore size, and pore shape on methane occurrence quantity. Finally, microscopic occurrence mechanisms of methane were explained by discussing the microscopic distribution characteristics of methane, the microscopic interaction characteristics between methane and pore walls, and the preferential adsorption sites of methane. The results showed that under deep high-pressure conditions, excess adsorption and dissolution of methane were relatively insensitive to temperature. As the temperature increased, both the absolute adsorption and free gas volume of methane decreased. The mesopore size of kerogen had almost no effect on the adsorption and dissolution of methane, and the changes in the total gas volume due to pore size were mainly contributed by free gas. In comparison to cylindrical pores, methane exhibited a higher total gas volume in slit-like pores, but the excess adsorption was lower. Methane molecules preferentially adsorbed at the thiophene sites on kerogen structure. The research findings provide a theoretical basis for estimating the reserves of deep shale gas.