Mining-induced fractures often constitute water inrush channels, which lead to mine water inrush accidents. In this paper, a coupled model of stress–seepage–damage based on micromechanics is established, which simulates the initiation and propagation of cracks in rock materials and their interaction with fluid flow. The method combines the continuous damage model with the effective stress principle, in which the elastic modulus and permeability are related to the damage variables. The model is implemented via the COMSOL code based on the finite element method, and the reliability of the model is verified by the axial compression–seepage test of standard rock samples. According to the actual geological conditions of F13 fault in Wugou Coal Mine, Anhui Province, the damage of the floor rock mass and the risk of fault water inrush in the 1033 mining face with 50, 40, 30, and 20 m waterproof coal pillars are predicted. When the coal pillar width is 30 or 20 m, the fault, the surrounding rock of the fault, and the failure zone of the floor constitute the water inrush channel. This model provides an intuitive understanding of the rock damage and water inrush evolution, which is difficult to observe, and will contribute to prevent water inrush disasters in practical engineering.