Two-phase flow remains a significant challenge in the development of water-bearing shale gas, particularly regarding the flow of gases through clay minerals in such formations. Nonequilibrium molecular dynamics simulation is investigated to research the two-phase flow of water (H2O) and methane (CH4) through Ca-montmorillonite (MMT) shale nanoslits. The results indicate that water molecules preferentially adsorb onto the surfaces of the Ca-MMT shale nanoslits, leading to the formation of water bridges within the nanoslits as water content increases. Notably, CH4 molecules exhibit complete solubility in the water phase, and their maximum velocity gradually decreases, resulting in a flattened parabolic flow profile with a higher gas-water percent (GWP). In the two-phase flow, CH4 continues to flow without slip in the inorganic nanopores due to water molecules occupying the surfaces and creating a water film. However, when the water content (GWP) exceeds 80.87%, CH4 gas molecules become dissolved in the water, filling the inorganic nanoslits and leading to a zero-gas flux. This condition causes CH4 retention in adjacent nanoslits, creating a "water lock gas" effect. This research provides a theoretical foundation for understanding multiphase flow in water-bearing shale gas and offers a refined description of the shale gas extraction process for future application.