The morphology of the joint surface is multi-scale, and it can be divided into first-order asperity (waviness) and second-order asperity (unevenness). At present, the joint roughness characterization formula considers only the morphology contribution of waviness and unevenness components and does not fully consider their mechanical contribution. At same time, the relationship between the mechanical contribution and the morphology contribution is still unclear. Thus, the characterization formula considering the mechanical contribution of waviness and unevenness needs to be further studied. In this study, the standard joint roughness coefficient (JRC) profiles were first decomposed into waviness and unevenness. Then, three types of joint specimens with different asperity orders (flat, the standard JRC profile, and the profile containing only waviness) were prepared by the 3D engraving technique. Finally, direct shear tests were carried out on 39 sets of red sandstone joint specimens under three normal stresses. The mechanical contributions of waviness and unevenness were studied, the relationship between the mechanical contribution and the morphology contribution of waviness and unevenness was analyzed, and the characterization formula considering the mechanical contribution of waviness and unevenness was established. The results showed that the following: (1) the method combining the ensemble empirical mode decomposition (EEMD) and the critical decomposition level could be used to separate the waviness and unevenness from the joint surface; (2) the mechanical contribution of the waviness and unevenness decreased with the increase in normal stress; (3) the relationship between the mechanical contribution ratio and the statistical parameter ratio of the waviness and unevenness can be describe by power function; and (4) the roughness characterization formula considering the mechanical contribution and morphology contribution was established. This study will enhance the accurate evaluation of the roughness coefficient and shear strength of the joint specimen.