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Modeling seepage problems in rock fractures is an interesting research approach to evaluating rock slope instability that is attracting increasing attention. In the present study, a coupled seepage–deformation model based on the numerical manifold method (NMM) is proposed, and the flow of groundwater in a fracture network coupled with the effects of seepage pressure and rock deformation are discussed. A global equilibrium equation of the system and a local factor of safety (FoS) of arbitrary rock fractures are derived based on the principle of minimum energy, and a series of verification examples are calculated. The simulation results show the robustness and effectiveness of the proposed numerical model. Finally, a rock slope collapse accident caused by seepage effects is simulated by the proposed method, and the failure process of the slope is reproduced. The simulation results show that excessive hydraulic pressure caused the vertical fractures to open and augmented the rock mass deformation, eventually leading to the failure of the slope. The proposed method possesses the potential to simulate larger-scale engineering problems.