The failure mechanism of heterogeneous rocks (geological materials), especially under hydraulic conditions, is important in geological engineering. The coupled mechanism of flow-stress-damage should be determined for the stability of rock mass engineering under triaxial stress states. Based on poroelasticity and damage theory, a three-dimensional coupled model of the flow-stress-damage failure process is studied, focusing mainly on the coupled characteristics of permeability evolution and damage in nonhomogeneous rocks. The influences of numerous mesoscale mechanical and hydraulic properties, including homogeneity, residual strength coefficient, loading rates, and strength criteria, on the macro mechanical response are analyzed. Results reveal that the stress sensitive factor and damage coefficient are key variables for controlling the progress of permeability evolution, and these can reflect the hydraulic properties under pre-peak and post-peak separately. Moreover, several experiments are conducted to evaluate the method in terms of permeability evolution and failure process and to verify the proposed two-stage permeability evolution model. This model can be used to illustrate the failure mechanics under hydraulic conditions and match different rock types. The relation of permeability with strain can also help confirm appropriate rock mass hydraulic parameters, thereby enhancing our understanding of the coupled failure mechanism in rock mass engineering.