Organic, ionic soil stabilizers (OISS) are designed to regulate directly the hydration properties of clay minerals to improve their engineering behavior. The steps involved in this regulation by OISS are unclear and this might limit their application in the current construction environment in China. The purpose of the present study was to reveal the origin of changes in hydration properties of four typical clay samples (with clay mineral contents of >90 wt.%: Na-bentonite, Ca-bentonite, illite, and kaolinite) as affected by OISS. The water-retention capacity of each clay was measured first through liquid limit and water-vapor adsorption tests. Then, the changes in hydration sites, such as exchangeable cations and the surfaces of minerals, were investigated by a series of microscopic measuring and testing techniques. Finally, infrared spectroscopy (IR) and thermal analysis were performed to verify the regulation of hydration properties by OISS. The results suggested that the exchangeable cation and surface changes controlled the regulation of hydration properties. OISS could cause some of the exchangeable cations to become free ions and disrupt the interaction between some cations and water molecules by its long organic chains; thus, the amount of hydrated cations decreased. In addition, the long organic chains covered the mineral surface and weakened its adsorption capacity. Furthermore, the long chains had cementitious qualities, connecting them to the crystalline layer and resulting in more aggregated clay particles and a smaller specific surface area (SSA). With the decrease in the number of cations and in the SSA by OISS, the hydration of the four clay samples decreased, especially in the case of bentonite.