<p>The deformation and instability of rock mass are primarily controlled by the shear strength of joints, which is strongly dependent on normal stress, joint roughness, and rock type. However, previous research findings on the shear strength of joints were almost all achieved under the condition of uniformly distributed normal stress. This conflicts with the actual normal stress state since the thickness of the overlying rock layer on the joint is usually uneven due to the influences of geological conditions and human factors, i.e., non-uniform normal stress. Therefore, this paper conducted the indoor direct shear tests under four kinds of non-uniform normal stresses on the rough joints to investigate the shear properties and the roughness evolution of joints under non-uniform loading. The results show that the shear characteristics are stable under uniformly distributed loading (UDL) and central distributed loading (CDL), while for left distributed loading (LDL) and right distributed loading (RDL), the eccentric load causes stress redistribution and concentration within the joint, leading to easier failure and larger peak shear displacement. With the increase of normal stress and roughness, the difference between the peak and residual strengths of joints nonlinearly increases. By comparing the morphology of the joints before and after shearing using 3D laser scanning, it was found that the joints with low roughness were most sensitive to the load distribution form. Under the right loading condition, roughness increased by 261.1%. This study reveals the evolution mechanism of shear strength of joints under non-uniform normal loads and its dynamic coupling with roughness characteristics, which provide a basis for the stability assessment and the construction of joint mechanical models of rock mass in complex stress fields.</p>