This study presents a three-dimensional discrete fracture network-fault (3D DFN-fault) model that contains a 3D DFN and a deformable 3D fault. The fault slip-induced shear displacement and normal displacement are taken into account. Under a constant normal stiffness (CNS) boundary condition, the normal displacement gives rise to an increase in the normal stress and a decrease in the aperture of the fractures connected to the fault, which are then incorporated into the model. Finally, a numerical code is developed to simulate fluid flow through the 3D DFN-fault model during shearing and the effects of the aperture heterogeneity, shear displacement and fracture structure on the hydraulic properties of fractured rock masses are estimated. The results show that an obvious channeling flow in the fracture networks is observed as remarkable localizations of the flow paths within limited areas of fracture planes. The aperture heterogeneity of fractures tends to hinder the overall flow through the DFN-fault model during shearing. The equivalent permeability decreases at the beginning of shear because of the stress-induced closure of fractures. With increasing the shear displacement, the equivalent permeability of the model in direction perpendicular to the fault slip direction either increases or decreases, depending on the competition of two effects: (i) the permeability is enhanced by the shear-induced dilation of the fault and the newly generated flow paths by connecting the dead-ends of fractures that are intersected to the fault; (ii) the permeability decreases due to the closure of fractures, which is influenced by the increase in the dilation-dependent normal stress. However, as the shear displacement continuously increases, the equivalent permeability in the direction parallel to the fault slip direction steadily increases.