The surface morphology of joints has a significant effect on the mechanical properties of rock masses. The key morphological indices developed in this study have been used to analyze the joint surface morphology quantitatively, and a new peak shear strength model has also been developed. Firstly, three-dimensional morphology scanning tests have been carried out on seven groups (27 blocks in total) of rock joints with different surface morphologies, and a new functional relationship between the apparent dip angle and the initial contact area ratio has been established: i.e. Aθ∗+=exp−θ∗/θ¯∗n, where Aθ∗+ is the contact area ratio, θ¯∗ is the characteristics angle, and n is a fitting parameter. The average joint height has been used to account for the effect of the joint fluctuation on the surface morphology. Ten standard roughness profiles have been digitalized to compute the roughness indices of each profile and to establish a relationship with the JRC (joint roughness coefficient). The direct shear tests have been carried out. By analyzing the test results, a new peak shear strength model has been developed. Comparing with the results from five classical models, the error between the calculated results of the new model and the experimental results is the smallest. Hence, the new model is a reliable tool for the estimation of the peak shear strength of rock joints.