In this paper, shale samples of Lower Silurian Longmaxi Fm, taken from the Changning–Weiyuan area in the Sichuan Basin, were selected to figure out the influence of reservoir primary water on the adsorption laws and the flow capacity of shale gas. Experimental samples with different water saturations were prepared using the adsorption equilibrium method. Then, high-pressure isothermal adsorption experiments were carried out, and the isothermal adsorption effects and mechanisms of shale under different water saturations were discussed. Finally, the flow capacity of shale gas under different water saturations was tested using the independently developed steady-state flow test device. And the following research results were obtained. First, the presence of primary water in micron–nanometer pores of shale reservoirs reduces the adsorption capacity of shale. When the water saturation is 40%, the simulated total gas content is 18% lower than that in the conventional calculation result. Second, the apparent shale permeability is a function of pressure. Due to the effect of Knudsen diffusion, the apparent shale permeability increases significantly with the decrease of pressure under low pressure. When the average pressure is 5 MPa and the water saturation reaches 50%, the apparent shale permeability is about 70% lower than that of a dry sample. Third, when the water saturation is lower than the critical value, water is mainly presented as non-movable water in micropores and mesopores, and it has less effect on the flow capacity of shale gas. When the water saturation is greater than the critical value, the lodging point of water is changed, resulting in significant reduction of the shale gas flow capacity. It is concluded that an accurate understanding of the original water saturation and critical water saturation of shale reservoirs helps to calculate shale gas reserves accurately and predict gas well production rate rationally.