The stress response and failure process of fractured rock mass in the karst development zone are more complex under the coupling effect of stress field and seepage field. The discontinuous numerical model considering hydraulics-mechanics coupling process is an important method to study the mechanism of tunnels water inrush. Discontinuous deformation analysis (DDA), based on rigorous contact description and convergence analysis, can account for the influence of intersecting cracks and the failure process caused by potential large deformations. On the basis of the original DDA method, a rock failure model was developed to analyze the seepage field and crack evolution in fractured rock mass by adding a fracture flow module and an excavation process simulation module. By simulating hydraulic fracturing experiments, the process of crack propagation in rock mass under hydraulics-mechanics coupling was analyzed, the validity of the seepage model was confirmed, and this model was applied to simulate the process of water inrush in tunnels under the effect of hidden karst caves. The influence of geo-stress level and relative position of karst caves on the propagation path and types of fractures, as well as the possibility of water inrush disasters was analyzed. The focus of preventing water inrush disasters in engineering activities was proposed, and the suggestions for safe tunnel construction were provided.