<p>Joints are critical structural planes that control the stability and seepage behavior of rock masses in deep underground engineering, and the evolution of their geometrical features directly affects both the mechanical and hydraulic properties of the surrounding rock. To investigate the influence of joint roughness on the shear–seepage characteristics of granite, shear–seepage tests were carried out on single-joint granite specimens with different roughness levels (JRC = 6–8 and 18–20) under normal stresses of 5, 10, and 15&#xa0;MPa. Scanning electron microscopy (SEM) was employed to examine the post-shear micro-morphology of the joint surfaces. The results show that both the peak shear stress and shear displacement increase with increasing normal stress. However, the increment in peak shear stress gradually decreases as joint roughness and normal stress increase. The initial permeability decreases with increasing joint roughness and normal stress. During shearing, the permeability–shear displacement curve exhibits a three-stage evolutionary pattern, characterized by an initial stable stage, a sharp increase stage, and a subsequent stabilization stage. Compared with high-roughness joints, low-roughness joints exhibit a more pronounced increase in permeability at shear failure; under a normal stress of 15&#xa0;MPa, the permeability can increase up to eight times that before the instability point. Roughness degradation occurs on all joint surfaces after shearing, with more pronounced deterioration in high-roughness specimens; their degradation ratio increases from 4.97% to 15.24% with increasing normal stress. In addition, SEM observations show that the number of microcracks and debris on the joint surface increases with increasing roughness. These findings highlight the controlling role of joint-surface morphological evolution in shear–seepage behavior and provide a reference for coupled hydraulic–mechanical analysis and stability assessment of fractured rock masses in deep geological environments.</p>