Chemical components of the soil take an important role in the structure stability. It controls the soil structure under the normal water environment such as ordinary temperature, atmospheric pressure, and slowly changing hydro-chemical environment etc. It also has an important influence on the ground subsidence and the formation of soil caves as well as the collapse of dispersive soil. Scanning Electron Microscopy(SEM), CT technology and X diffraction were used to measure the chemical damage of water to the soil structure in the laboratory. Results indicate that under normal water environment, the change of the environmental parameters is not sufficient to cause damage to the internal crystal force of mineral intergranulars and to activate atoms in crystal lattice, which leads some defects and displacement of the crystal lattice. However, it can activate linking substance of clay grains be defined as “soil mini-structure”. As the greatest contributor of soil stability, the mini-structure is the "platform" and main place in which soil stability and instability will develop.