Although boundary conditions can significantly impact the shear behaviors and asperity damage evolution of jointed rocks, numerical studies on the damage of 3D rough rock joints under the constant normal stiffness (CNS) boundary condition have rarely been reported. In this work, the three-dimensional model of the irregular joint surface is established by using point cloud reconstruction technology. Based on the cohesive zone model (CZM), we simulate the shear behavior of three-dimensional rough rock joints under the CNS boundary condition, which is realized by using embedded spring elements implemented with a Python subroutine. We conducted laboratory direct shear tests under CNS boundary conditions. The agreement with the laboratory experimental results verifies the fidelity of the numerical method. Our results show that boundary conditions can significantly affect the shear behavior of rock joints, especially in the post-peak stage. Under the same initial normal stress, the peak shear stress and the number of microcracks in the asperities increase significantly with the increase of normal stiffness. The proportion of shear cracks positively correlates with the normal stiffness, indicating that the normal stiffness affects the joint failure mode. The damaged area and the volume of asperities increase with the increase of normal stiffness. Moreover, the distribution of shear-induced asperity loss becomes more nonuniform, and the loss of joint roughness increases rapidly and nonlinearly.