Purpose: To evaluate multiple risk factors for peri-implant bone loss via a statistical analysis with a multivariate logistic regression model to provide recommendations for clinical treatment. Materials and Methods: This case-control study was conducted on patients who had received dental implant treatment from January 2018 to December 2021. Patients who had implants with bone loss were included in the case group, and patients who had implants with no bone loss were included in the control group. The following risk factors were evaluated: history of periodontitis, abutment connection type, implant surface type, implant diameter, implant location, implant 3D position, opposing dentition, adjacent teeth, prosthetic type, retention type, and the use of custom abutments. A multivariate logistic regression model was used to evaluate these risk factors, providing corresponding odds ratios (ORs) and 95% CIs. Results: A total of 776 implants in 479 patients were included in the analysis. The number of implants in the case group and the control group were 84 and 692, respectively. Cement-retained prostheses (OR = 2.439, 95% CI = 1.241–4.795) and non-platform-switched designs (OR = 2.055, 95% CI = 1.167–3.619) were identified as weak risk factors. Horizontal deviation (OR = 4.177, 95% CI = 2.265–7.703) was demonstrated to be a moderate risk factor. Vertical deviation (OR = 10.107, 95% CI = 5.280–19.347) and implants located in the mandibular molar region (OR = 10.427, 95% CI = 1.176–92.461) were considered high risk factors. Conclusions: Implants in the molar region, cement-retained prostheses, non-platform-switched designs, and poor 3D implant positioning were identified as significant risk factors for peri-implant bone loss.