Due to the existence of water content in shale reservoir, it is quite meaningful to clarify the effect of water content on the methane adsorption capacity (MAC) of shale. However, the role of spatial configuration relationship between organic matter (OM) and clay minerals in the MAC reduction process is still unclear. The Silurian Longmaxi Formation shale samples from the Southern Sichuan Basin in China were prepared at five relative humidity (RH) conditions (0%, 16%, 41%, 76%, 99%) and the methane adsorption experiments were conducted on these water-bearing shale samples to clarify the MAC reduction process considering the spatial configuration relationship between clay minerals and OM and establish the empirical model to fit the stages. Total organic carbon (TOC) content and mineral compositions were analyzed and the pore structures of these shale samples were characterized by field-emission scanning electron microscopy (FE-SEM), N₂ adsorption and high-pressure mercury intrusion porosimetry (HPMIP). The results showed that the MAC reduction of clay minerals in OM occurred at different RH conditions from that of clay minerals outside OM. Furthermore, the amount of MAC reduction of shale samples prepared at the same RH condition was negatively related with clay content, which indicated the protection role of clay minerals for the MAC of water-bearing shale samples. The MAC reduction process was generally divided into three stages for siliceous and clayey shale samples. And the MAC of OM started to decline during stage (1) for calcareous shale sample mainly because water could enter OM pores more smoothly through hydrophobic pathway provided by carbonate minerals than through hydrophilic clay mineral pores. Overall, this study will contribute to improving the evaluation method of shale gas reserve.