In order to explore the microscopic storage mechanism of shale gas in waterbearing pores and its influencing factors, this article first establishes a molecular dynamics model for methane in different types of adsorbents using molecular dynamics simulation and the grand canonical ensemble Monte Carlo methods. These adsorbents include graphene, organic matter (kerogen), brittle minerals (quartz and albite), carbonate minerals (calcite), and clay minerals (illite, kaolinite, and montmorillonite). Then, by analyzing the molecular storage model and density distribution curves of methane in pores, the storage mechanisms of shale gas are analyzed and elucidated. Finally, the effects of pore water, organic/inorganic composition, pore size, pore shape, temperature, pressure, salinity, organic matter type, and multicomponent mixed gases on shale gas storage are discussed. This work aims to provide theoretical and technical support for the evaluation, exploration, and development of shale gas.