The shale gas adsorption and flow characteristics play essential roles in improving shale gas recovery. Motivated by the desire to clarify these characteristics carefully and precisely, a series of shale models with different water contents from 0.6 to 2.4 wt% were established. Presumably, these characteristics were sought to pin down answers by using the grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) methods respectively. Importantly, the analysis of the pore structure of these models is firstly taken into account considering its microstructure to meet the demand for the explanation of the adsorption characteristics of methane. The results showed that the enterable volumes decrease significantly with the increase of water content due to the diffusion and aggregation of water molecules in the middle of enterable pores. Intuitively, it could lead to a marked linear decrease in the adsorption amount of methane from 1.2 mmol/g to 0.6 mmol/g. A curiosity of this study is that the diffusion coefficients of methane increase as the increase of temperature and ensuring the low pressure outside the channel could boost the flux of methane intriguingly. Suffice to say, the optimum development shale gas conditions in this work are at the temperature of 358 K and in the presence of water content of 2.4 wt%. Hence, there is an expectation that this study would provide a guidance for the exploitation of shale gas in the presence of water.