Abstract: The water adsorption by shale significantly affects shale gas content and its seepage capacity. However, the mechanism of water adsorption by shale is still unclear due to its strong heterogeneity and complicated pore structure. The relationship between the adsorbed water content at different relative humidities (RHs) and shale compositions, as well as shale pore structure and the spatial configuration relationship between organic matter (OM) and clay minerals, was investigated to clarify the controlling factors and mechanisms of water adsorption by Longmaxi Formation shale from the Southern Sichuan Basin in China. Consequently, the water adsorption process could be generally divided into three different stages from 0%RH to 99%RH. Furthermore, the Johnston's clay mineral interlayer pore structure model (JCM), the Freundlich model (FM) and the Dubinin–Astakhov model (DAM) were tested to fit the three water adsorption stages from low RH to high RH, respectively. The fitting results of the JCM and FM at lower RHs were far from good, while the fitting results of DAM at higher RHs were acceptable. Accordingly, two revised models (LRHM and MRHM) considering the spatial configuration relationship between OM and clay minerals were proposed for the two stages with lower RHs, and performed better fitting results indicating the pronounced effect of the spatial configuration relationship between OM and clay minerals on the water adsorption process of Longmaxi Formation shale. The outcomes of this study will contribute to clarifying the water distribution characteristics in the pore network of shale samples with variable water contents.