<p>The coupling behavior of seepage and shear stress in rock fractures is critical to hydrogeology and geomechanics. However, the mechanisms behind this interaction are complex and difficult to investigate. This study examines how shear and normal stresses affect seepage in fractured rocks. Three groups of fracture surfaces with different geometric properties were scanned to obtain the average joint roughness coefficient (JRC) for each group, and through shear–seepage–stress coupling tests, the seepage characteristics and movement patterns of random single fractures under seepage conditions were analyzed, considering the combined effects of normal compressive stress, shear load, and seepage pressure. Meanwhile, by analyzing the hydraulic aperture test data, the relational expressions between the average JRC value, normal pressure, seepage pressure, and peak equivalent hydraulic aperture were derived. Finally, the laws governing how factors such as seepage pressure, roughness, and normal pressure affect normal displacement, shear load, and equivalent hydraulic aperture during the shear–seepage coupling process were summarized. Results show consistent displacement patterns for shear–seepage coupling across all specimen groups, with well-fitted results. Shear-induced fracture displacement generates a reactive force against normal pressure, thereby aiding debris removal in seepage channels. This effect varies with surface roughness, as rough fractures show greater displacement than smooth ones. The inhibitive effect of normal pressure on vertical displacement during shearing is nonuniform, depending on fracture roughness. These findings provide new insights into the interaction between shear stress and fluid flow in fractured rock, with implications for predicting fluid transport and solute migration in subsurface environments.</p>