The instability of jointed rock mass is usually the shear process of the rock mass along discontinuities under the influence of groundwater flow. By conducting laboratory tests and numerical experiments on the shear-flow coupling of rock joints under constant normal stiffness (CNS) and constant normal stress (CNL) boundary conditions, the influence of normal boundary conditions and seepage pressure on the shear mechanical and flow characteristics of joints were investigated. The test results were as follows: The joint shear stiffness, peak, and residual shear strength under the CNS boundary condition were predominantly larger than those under the CNL boundary condition. Overall, these parameters were positively correlated with the initial normal stress σ n 0 . When σ n 0 > 2 MPa, the postpeak shear stress of the CNS boundary condition showed a sharp decrease, whereas that of the CNL boundary condition changed from a slowly decreasing type ( σ n 0 = 4 MPa, 6 MPa) to a sharply decreasing type at σ n 0 = 8 MPa. The peak dilation rate under the CNS boundary condition at all levels of normal stress was lower than that of CNL, and the strain softening in postpeak of the latter was more remarkable. In the process of joint shear, the hydraulic aperture displayed a four-stage variation law of “steady-sudden increase-slow increase-basically stable.” Moreover, the hydraulic aperture under the CNS boundary condition was always lower than that under the CNL boundary condition. The seepage pressure increased from 0.5 MPa to 1.5 MPa, and the average hydraulic aperture in the stable stage under normal stress at all levels increased from 0.146 mm to 0.187 mm. In addition, the average peak shear stress and average shear stiffness decreased by 0.9 MPa and 0.83 GPa/m, respectively. We also established a numerical model of a real rough three-dimensional joint, compiled a calculation program for the shear-flow process of a joint under CNS boundary conditions, and visualized the flow channel inside the joint. The seepage flow bypassed the area where the joints contacted each other, forming obvious flow channels. The flow rate increased at the intersection of the flow channels.