In recent years, with the depletion of traditional fossil energy, shale gas, as a major kind of unconventional reservoir, plays a more and more core role in global energy pattern. Nevertheless, contrary to conventional reservoirs, shale is nanoporous rock with ultra-low porosity and nanoscaled pores. Previous attempts to characterize methane gas flow in shale nanopores are not fully successful due to that the presence of water within shale nanopores is generally overlooked. Herein, we performed a comprehensive study of methane gas flow behavior in moist shale nanopores (organic: hydrophobic; inorganic: hydrophilic) by integrating the molecular dynamics (MD) simulations and analytical model. Using MD simulations, we showed that water molecules prefer to accumulate at the walls (water film) in hydrophilic nanopores while form water cluster at center region of hydrophobic nanopores, which significantly alters the methane gas flow behavior. For hydrophilic nanopores, the existence of water film weakens the gas-walls collisions (slip effect), resulting in a viscosity dominant flow mechanism. In contrary, methane gas flow in hydrophobic nanopores is mainly contributed by slip effect where the gas-gas collisions (viscosity) is abated by the water cluster. On this basis, we proposed an analytical model to quantitatively depict the methane gas flow behavior in moist shale nanopores considering the coupling of solid-liquid boundary and liquid-gas boundary interactions, which is well verified by MD simulations results. Particularly, according to our flow model, the gas transport capacity decreases to only 15% when mixing with 50% water molecules for both hydrophilic and hydrophobic nanopores, which would be greatly overestimated by traditional models neglecting the presence of water molecules. This work shows the necessity of MD simulation in nanoflow field and the deep insights gained in this work will further the exploitation and development of shale reservoirs.