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To explain the effect of joint roughness on joint peak shear strength (JPSS) and investigate the effect of different contact states of joint surface on JPSS, we try to clarify the physical mechanism of the effect of joint cavity percentage (JCP) on JPSS from the perspective of the three-dimensional (3D) distribution characteristics of the actual contact joint surface, and propose a JPSS model considering the JCP. Shear tests for red sandstone joints with three different surface morphologies and three different JCPs were performed under constant normal load condition. Based on test fitting results, the reduction effect of the JCP on JPSS is investigated, and a JPSS model for cavity-containing joints is obtained. However, the above model only considers the influence of JCP by fitting test data, and does not reveal the physical mechanism of JCP affecting the JPSS. Based on the peak dilation angle model for consideration of the actual contact joint morphology, and the influence of JCP on the roughness of the actual contact joint surface, a theoretical model of the JPSS considering the JCP is proposed. The derivation process does not depend on the test fitting, but is entirely based on the joint mechanical law, and its physical significance is clear. It is proposed that the essence of the influence of the JCP on JPSS is that the JCP first affects the normal stress of the actual contact joints, further affects the roughness of actual contact joints, and then affects the shear strength.