Many studies have been carried out to investigate the scale effect on the shear behavior of rock joints. However, existing methods are difficult to determinate the joint roughness coefficient (JRC) and the shear strength of rock joints with incomplete and indeterminate information; the nature of scale dependency of rock joints is still unknown and remains an ongoing debate. Thus, this paper establishes two neutrosophic functions of the JRC values and the shear strength based on neutrosophic theory to express and handle the incomplete and indeterminate problems in the analyses of the JRC and the shear strength. An example, including four rock joint samples derived from the pyroclastic rock mass in Shaoxing city, China, is provided to show the effectiveness and rationality of the developed method. The experimental results demonstrate that the proposed neutrosophic functions can express and deal with the incomplete and indeterminate problems of the test data caused by geometry complexity of the rock joint surface and sampling bias. They provide a new approach for estimating the JRC values of the different-sized test profiles and the peak shear strength of rock joints.