Deep-buried hydraulic tunnels are usually constructed under the condition of high groundwater level. To accurately evaluate the deformation stability of the surrounding rock, it is necessary to reasonably simulate the mechanical effect of external water infiltration. Although it has been recognized that rock matrix compressibility should be taken into account in the seepage-stress coupling analysis of saturated rocks, there is still lack of relevant research on the effects of rock matrix compressibility on the deformation stability of hydraulic tunnels under high external water pressure. Based on the effective stress principle of saturated porous medium and pore pressure correction coefficient, a seepage-stress coupling model of hydraulic tunnels under high external water pressure is proposed with the consideration of the permeability variation of surrounding rock during its deformation process. Then, the proposed model is implemented in ABAQUS, and the seepage field and deformation stability of a deep-buried diversion tunnel is studied under different conditions of rock matrix compressibility. Numerical simulation results show that rock matrix compressibility directly affects the external water infiltration process, and it is unfavorable to the deformation stability of the hydraulic tunnel under high external water pressure. The greater the compressibility of the rock matrix, the larger the deformation and plastic zone of the surrounding rock. This indicates that the deformation stability evaluation of surrounding rock of the hydraulic tunnel under high external water pressure without considering the rock matrix compressibility will lead to incorrect results which will affect the safety of the tunnel.