Permeability evolution of natural fractures during shearing is one of the critical issues in enhanced geothermal system (EGS). In this study, we conducted a series of numerical simulations of shear-flow tests under different normal stresses to investigate the permeability evolution and shear behavior of natural fractures during shearing. All numerical simulations in this study are executed based on a coupled hydro-mechanical pore network model (PNM) for fluid flow within the discrete element method (DEM). The numerical model uses a 33 mm × 25 mm fracture surface profile extracted from X-ray computed tomography scanning data of joints in a rock core retrieved from a 4.2-km-deep well at the Pohang EGS site. The results demonstrate a positive correlation between fracture permeability and shear displacement when the normal stress is relatively high. The central aspect of permeability evolution lies in the variation of local aperture distribution along the pathway: an increase in the variance of fracture aperture distribution leads to an increase in fracture permeability. Permeability evolution of fractures is significantly affected by normal stress, fracture roughness, and relative flow direction. Larger fracture roughness facilitates the formation of high-permeability pathways. Higher local normal stress often corresponds to lower local permeability. Moreover, high normal stress amplifies the effect of fracture roughness on permeability evolution. These findings enhance our comprehensive understanding of hydraulic-mechanical coupling effects during EGS stimulation.