The JRC-JCS model, which is widely used in the field of geotechnical engineering, has the following defects: 1) the two-dimensional joint roughness coefficient (JRC) can’t comprehensively represent the anisotropy of joint surface morphology; 2) the joint compressive strength (JCS) of joint wall can’t entirely reflect the influence of material properties on joint shear mechanical behavior. In this paper, artificial joint samples with natural joint morphology were poured based on three-dimensional laser scanning and three-dimensional printing technology, and shear tests under constant normal stress were carried out. The shear strength model with three-dimensional morphology parameters and tensile strength parameters was established based on the analysis of experiments and theoretical derivations. The impacts of normal stress and three-dimensional morphology of fracture surface on shear strength and dilatancy angle of rock joints were analyzed through laboratory tests and model comparison. The results show that the shear failure of joints is dominated by tension rather than compression. The different three-dimensional morphology causes different initial dilatancy angles. The peak dilatancy angle decreases with the increase of the normal stress. The shear strength of rock joints can be calculated by studying the changes of the peak dilatancy angle.