The complex structural systems within rocks are random and disordered, so it is still a challenge to determine the relationship between microscopic junctions and macroscopic mechanical structural properties. More importantly, the origin of microstructure evolution in multiscale evolution has not been explained in detail. Water is the most abundant molecule found on the Earth's surface, so rocks exposed to water are everywhere, and the wetting, soaking and drying environment involved is one of the most critical factors leading to rock mass deformation and destruction. The drying-wetting cycle in a water environment accelerates the deterioration of the rock mass. By means of Nuclear magnetic resonance (NMR), high-precision X-ray microcomputed tomography (μCT) and SEM-energy dispersive spectroscopy (EDS) tracking observations in the same area, detailed evolution information of different stages in the rock interior was obtained, and the evolution mechanism of the microstructure was analyzed at the molecular scale. The dissolution of dolomite minerals during the interaction between rock and deionized water is very weak and does not play a key role in the rock failure process, as previously reported. Water molecules form an ordered adsorption structure with a high-density hydrogen bond network on the surface of hydrophilic clay minerals and dolomite, which induces the swell shrinkage of the hydrophilic clay aggregate structure and the expansion of the dolomite fracture tip, resulting in increased pore-fracture connectivity and decreased rock mechanical properties. In particular, the capillary force repeatedly acts on the crack tips of dolomite minerals under wetting and drying, further aggravating the damage to the rock structure. In this study, tracking observations in the same area reduce the randomness of obtaining the evolution information of microstructure characteristics, which is very important for further analysis of the relationship between multiscale evolution. Without such detailed and comprehensive evolution information, it is difficult to understand the essential mechanism of the multiscale evolution of rocks.