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Fractured seepage is an important factor affecting the interface stability of rock mass. It is closely related to fracture properties and hydraulic conditions. In this study, the law of seepage in a single fracture surface based on modified cubic law is described, and the three-dimensional discrete element method is used to simulate the dam foundation structure of the Capulin San Pablo (Costa Rica) hydropower station. The effect of construction joints and developed structure on dam stability is studied, and its permeability law and sliding stability are also evaluated. It is found that the hydraulic-mechanical coupling with strength reduction method in DEM is more appropriate to use to study the seepage-related problems of fractured rock mass, which considers practical conditions, such as the roughness of and the width of fracture. The strength reduction method provides a more accurate safety factor of dam when considering the deformation coordination with bedrocks. It is an important method with which to study the stability of seepage conditions in complex structures. The discrete method also provided an effective and reasonable way of determining seepage control measures.