The permeability prediction for fractured rock mass is the basis for analyzing permeability problems such as oil and gas exploitation, pollutant migration, and so on. In this paper, the in-house sub-element program was used to solve the steady-state Navier-Stokes equation for incompressible viscous flow. The periodic boundary conditions (PBC) were introduced to eliminate the error induced by choosing only a small section of fracture and ignoring the extension length of fracture in the previous numerical simulation. This method was applied to explore the effects of joint roughness coefficient (JRC), fracture width and mutual dislocation of two surfaces of fracture on permeability. The results show that the influence of JRC value on permeability decreases as the fracture width grows; the permeability of fractures cannot be accurately evaluated by using JRC values only.