A 3D equivalent continuum coupling analysis of the slope of the Zhouning pumped storage power station was proposed in this study. Firstly, the hydraulic properties of rock mass, groundwater, and deformation mechanism under high-frequency fluctuations of the water level are analyzed. Secondly, the three-dimensional Digital Terrain Model (DTM) with surface image information was established by digital photogrammetry technology for cataloging field fracture information. Third, stress-seepage coupling simulation using a hybrid grid approach and the FLAC3D equivalent continuum model was implemented. The results show that the permeability of rock mass is stress-dependent and anisotropic, and the direction of maximum principal permeability of both bank slopes is approximately parallel to the river. Slope deformations induced by impoundment during the operation period are the superposition results of two mechanisms, referred to as “mattress effect” and “swelling effect.” Attention should be paid to the tensile strength of the rock mass during operation.