The emergence profile (EP) of an implant restoration plays an essential role in stabilizing peri-implant tissues. However, to date, relatively few studies have focused on EP, particularly in the posterior regions. This prospective randomized controlled study observed and compared changes in peri-implant tissues between customized and traditional EPs. After re-open surgeries, 40 patients who accepted implant placement in molar sites with supracrestal mucosal thickness ≥ 3 mm were randomly assigned the test or regular group. Clinical data were collected 1 week after reopening surgery (T0), before and after computer-aided design/computer-aided manufacturing abutment placement (T1a and T1b), before and after definitive restoration placement (T2a and T2b), and 6 months after loading (T3). Radiographic data were recorded at T2b and T3. Changes in gingival width and papilla height in the test group were greater than those in the regular group from T2b to T0. The papilla height, papilla proportion, papilla index score, and black triangles were significantly ameliorated in the test group at T2b. Changes in papilla height, plaque index, patient satisfaction, and food impaction at T3 significantly improved in the test group. However, there were no significant differences in marginal bone loss between the two groups at T3. In summary, customized EP effectively increased the papilla height and decreased the risk of black triangles and peri-implantitis; thus, it is a potential alternative option for prosthodontists.