The excavation simulation and fully-coupled model of the fractured rock in the discrete element method are used to analyze the changes in fracture aperture and in the seepage flow process after excavation. The flowing discharge after tunnel excavation is used to represent the permeability of the fractured rock mass in the article, in order to investigate the coupling effect on the permeability characteristics of the fractured rock mass. The effect on flowing discharge in the excavated cavity or tunnel by block boundary size, initial in-situ stress ratio, the fracture aperture and the included angle were studied based on the numerical test. It is found that with the increase of block size and the in-situ stress ratio, the flowing discharge in the excavated tunnel becomes decreasing; and with the increase of initial hydraulic aperture, the flowing discharge increases coincidently and keeps invariant with a fixed amount. The flowing discharge reaches the maximum value when the included angle between the two joint sets is 75.