During the drilling in shale reservoirs using water-based drilling fluids, shale hydration leads to various risks such as wellbore collapse and stuck drills. However, the mechanism of shale hydration remains unclear. This work presents a comprehensive experimental investigation on the mechanisms of shale hydration using core samples of Sichuan shale (China), with a high content of illite. The impact of shale hydration on the stability of a borehole wall is presented by conducting fracture development tests, rock compressive strength experiments, SEM analyses, expansion tests, infrared analyses, and thermogravimetric analyses. Owing to the high content of illite and absence of smectite in the target shale formation, hydrogen bonding force between free/self-associated hydroxyl groups on rock surfaces and their neighbouring water molecules was observed as the primary factor that induces shale hydration. In comparison to the hydration mechanisms of mudstone, fewer hydrogen molecules bond with shale rock surfaces; however, a strong bonding force could result in the rapid hydration of the shale. For example, the hydration rate of shale 1.7 times greater than that of mudstone within the first 10 min was observed in our experiments. For this reason, the conventional inhibitors fail to prevent the surface hydration of shale rocks, and they can only protect rocks with percolation hydration. Therefore, the results of this work provide a unambiguous criteria for the development of novel inhibitors that can completely prevent shale rock hydration.