The extraction of impacted mandibular third molars might cause large bone defects in the distal area of second molars. A new strategy was innovatively employed here combining autologous bone, Bio-Oss, concentrated growth factors (CGF) gel and CGF membrane for bone repair, and the present study aimed at exploring safety as well as short- and long-term efficacy of this new protocol clinically.A total of 66 participants were enrolled in this randomized single-blind clinical trial, and randomly allocated to control group (only blood clots), test A group (autogenous bone, Bio-Oss with barrier membrane) and test B group (autogenous bone, Bio-Oss, CGF gel with CGF membrane). The postoperative outcomes including PoSSe scale, periodontal probing depth (PD), degree of gingival recession and computed tomography measurements were assessed at 3rd, 6th, 12th month. A p-value < 0.05 was considered statistically significant.In PoSSe scale, no significant difference was observed except a significant alleviation of early-stage pain perception in test B group (p < 0.05). Also, test B group exhibited better effect on periodontal healing and gingival recession reduction after 6 months (p < 0.05). Both two test groups showed more new bone formation than the control group (p < 0.05). It is noteworthy that the bone repair of test B group was significantly better than that of test A at 3rd and 6th month (p < 0.05), yet no difference was observed at 12th month (p > 0.05).Both two test groups could achieve stable long-term efficacy on bone defect repair. The use of CGF gel and CGF membrane could accelerate early-stage bone repair, alleviate short-term pain after surgery, reduce long-term probing depth and relieve economic cost for patients. This new bone repair protocol is worthy of promoting by clinicians.This study was registered with the identification number ChiCTR2300068466 on 20/02/2023 at Chinese Clinical Trial Registry. Also, it was ethically approved from the institutional ethics committee at the Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China (No:2023-010-01), and has been conducted in accordance to the guidelines of the declaration of Helsinki. Written informed consent was obtained from all participants in the study.© 2023. BioMed Central Ltd., part of Springer Nature.