Objective To explore the effect of cone-beam CT (CBCT) combined with warm gutta-percha technique on root canal obturation quality in patients with C-shaped root canal of mandibular second molar. Methods A total of 100 patients with C-shaped root canal of mandibular second molar admitted to Shanghai Jing'an Dental Clinic from January 2022 to January 2025 were selected, and they were divided into the control group and the observation group by the random number table method, with 50 patients in each group. The control group was treated with CBCT combined with cold gutta-percha lateral condensation technique, and the observation group was treated with CBCT combined with warm gutta-percha technique. The clinical efficacy, root canal obturation quality, complication rate and root canal treatment-related indicators were compared between the two groups. Results The total effective rate of the observation group (98.00%) was higher than that of the control group (82.00%) (P<0.05). The adequate obturation rate of the observation group was higher than that of the control group, and the under-obturation rate was lower than that of the control group (P<0.05). There was no statistically significant difference in the over-obturation rate between the two groups (P>0.05). The incidence of complications in the observation group (4.00%) was lower than that in the control group (20.00%) (P<0.05). After treatment, the distance between the filling material and the apical area and the root canal filling time of the observation group were shorter than those of the control group (P<0.05). Conclusion The application of CBCT combined with warm gutta-percha technique in the treatment of C-shaped root canal of mandibular second molar can improve clinical efficacy and root canal obturation quality, optimize treatment-related indicators, and effectively reduce the incidence of complications.