At present, the commonly used numerical reconstruction methods for digital cores are based on the scanning electron microscopy (SEM) images or CT scanning results obtained at atmospheric pressure, which is unrepresentative of the condition of the formation. It is not conducive to analyzing the pore structure of shale and simulating the flow of shale gas in digital rocks. In this paper, a displacement calculation model of shale matrix mineral and organic components has been established based on two dimensional digital rock and rock elastic mechanic equations. The pore structure of the digital rock model was modified under confining stress and pore stress. The effect of stress on pore structure of shale has been studied using the displacement calculation model. The simulation results indicate that the nano pores in organic components are more sensitive to stress. For the  slinpores, the displacement along the minor axis is bigger than that along the major axis under stress, which induces the long pores to close or to form some isolated pores. The pore pressure has more significant effect on nano pores, which will affect the shale gas flow in nano pores. The modification of digital core provides an accurate flow path for the future study on shale gas micro seepage flow using the lattice Boltzmann method.