The study aimed to stratify the risk of inferior alveolar nerve injury (IANI) after lower third molar (LM3) surgery with a scoring system using identified predictive factors based on cone-beam computed tomography (CBCT) images. In a case–control study, the primary outcome was IANI occurrence. The control group included randomly selected patients without IANI. Predictor variables included patient demographics, surgical situations, Pell–Gregory classification, and inferior alveolar canal (IAC)-associated factors on CBCT. Study variables were analyzed using logistic regression models. Risk stratification was assessed by a scoring system that was constructed using independent predictors. The 858 patients who underwent LM3 surgery (1177 teeth) after CBCT scan were divided into case (25 patients, 2.9%, 27 teeth) and control (235 patients, 300 teeth) groups. In the multivariate model, lingual/inter-radicular position of IAC [odds ratio (OR) 7.21; P?<?0.001; assigned score, 2], multiple roots closed to the IAC with cortical perforation (OR 3.72; P?=?0.015; 1), and age?>?30 years (OR 4.99; P?=?0.008; 2) were associated with an increased IANI-risk. The IANI-risk scoring system could be stratified into low- and high-risk groups at a cutoff score of 3 (sensitivity, 68.0%; specificity, 90.6%; positive predictive value, 17.8%; positive likelihood ratio, 7.23). In conclusion, the high-risk group of IANI after LM3 surgery corresponded to individuals with multiple factors: lingual/inter-radicular IAC position to LM3, multiple roots with perforated IAC, and increased age (>?30 years). Raising awareness of the higher probability for IANI is needed for patients with multiple aforementioned factors.