The action of freeze–thaw (F–T) cycles of claystone exerts a profound impact on the slope stability of open-pit mines in water-rich regions. Microstructural changes are observed as a crucial factor in determining the hydraulic characteristics and mechanical behaviors of claystone. The present work integrates a micro-X-ray computed tomography (Micro-CT) scanner, equipped with image processing and three-dimensional (3D) reconstruction capabilities, employed to observe the microstructure of claystone under varying numbers of F–T cycles (0, 10, 20, 30, and 50). Furthermore, seepage numerical simulations based on Micro-CT measurements are conducted to evaluate the hydraulic characteristics. Through meticulous microscopic observation and mechanical analysis, the damage mechanism induced by F–T cycles is revealed and the evolutionary characteristics are analyzed. The two-dimensional (2D) images of 3D reconstructed models unveil the gradual initiation propagation and coalescence of an intricate fissuring network in claystone during the F–T cycles. As the number of F–T cycles increases from 0 to 50, the 3D porosity exhibits exponential growth. Additionally, the influence of F–T cycles substantially enhances the connectivity of fissures. The seepage numerical simulations demonstrate that the evolutionary progression of fissures substantially augments the number of flow paths and enhances permeability. The increase in permeability follows an exponential trend, reflecting the distribution and evolution of fissures under F–T cycles. The impact on permeability arises from a combination of micromechanical properties and the microstructure of claystones. The present research tries to elucidate the microscopic evolution of fissures and their corresponding hydraulic properties in water-saturated claystone, offering significant insights for investigating the slope stability of open-pit mines in regions.