Mudstone material in a deep roadway is under the coupled stress-seepage condition. To investigate the permeability change and damage development during rock excavation in roadways, a stress-seepage damage coupling model has been proposed. In this model, damage capacity expansion of mudstone material is considered as the initiation and propagation of micro-cracks and the fracture penetration. A damage variable is introduced into the proposed model based on the principle of minimum energy consumption. As a result, an elastoplastic damage constitutive equation is established. Then, the permeability evolution equation describing the micro-macro hydraulic behavior of mudstone is deduced via percolation theory, which can describe the characteristics of sudden permeability change after rock capacity expansion. Furthermore, a finite element model is established based on commercial finite element software-ABAQUS. The numerical model was firstly verified by comparison between experimental and simulation results. On the basis of it, numerical investigation of the temporal and spatial evolution law of pore pressure, damage and permeability coefficient during roadway excavation is undertaken. The numerical results indicate that with increase of construction time, pore pressure first increases and then decreases, while the damage zone and permeability coefficient increase gradually and finally nearly keep constant. The proposed coupling model and finite element method can describe damage and permeability evolution for mudstone material under coupled stress-seepage well.