The rock of the dam is supposed to be dual-porosity medium and pore pressure in fracture and micro-pores are coupled with the stress in dam. The evolution of the permeability is studied by analyzing the hydraulic pressure and the deformation of the rock. Mathematical models are built to quantify the fluid flow, the deformation of rock skeleton and the net change of permeability. The relations between the pore pressure and permeability (porosity)are also been analyzed and they offer new ideas to solve dam stability problems in engineering.