Purpose: Prosthesis design, which affects the stress distribution and plaque control in the interproximal area between two adjacent implants, was a key-factor in the success of implant treatment, especially in the posterior region of the jaw. The aims of this study were to analyze and compare the long-term prognosis of splinted and nonsplinted types of implant-supported prostheses in the human molar region. Materials and Methods: We analyzed 242 implants (121 sites) installed in the first and second molar regions in 102 patients. Implants were divided into splinted and nonsplinted groups. For each group, sex, age, implant position, bone grafting, functional loading periods (FLP), clinical crown/implant (C/I) ratio, crown height space (CHS), horizontal distance between implants, prosthesis types, and occurrence of complications were investigated. Results: Mechanical complications were observed at 9 sites in the splinted group and 2 sites in the nonsplinted group. Biological complications occurred at 16 sites in the splinted group and 5 sites in the nonsplinted group. In splinted group, a statistically significant relationship was found between biological complications and longer FLP, lower clinical C/I ratio, and lower CHS. In the nonsplinted group, mechanical complications were statistically significantly associated with lower CHS. The cumulative risk of biological complications increased dramatically from 90.33 months of FLP in the splinted group. Conclusion: Lower CHS was the most important cause of biological complications for splinted implants and of mechanical complications in the nonsplinted implants. An FLP of 90.33 months could be used as a reference time point for follow-up visits to identify and prevent biological complications in splinted implants.