Objective To analyze the value of CBCT in evaluating the root and root canal anatomy of mandibular second molars. Methods A retrospective study was conducted on 610 patients with mandibular second molars who underwent CBCT imaging examination in our hospital from May 2020 to May 2022. The root and root canal morphology and distribution of mandibular second permanent molars in 610 patients, the root number, root canal number and distribution of mandibular second permanent molars with non-C-shaped roots in 356 patients, and the root canal configuration distribution of mandibular second permanent molars with double roots in 312 patients were retrospectively analyzed. Results There was no statistically significant difference in the root morphology between the left and right mandibles, as well as between males and females ( P >0.05). There was no statistically significant difference in the detection rate of C-type root canals between the left and right mandibles, as well as between males and females ( P >0.05). There was no statistically significant difference in the number of teeth roots between the left and right mandibles, as well as between males and females ( P >0.05). There was no statistically significant difference in the number of root canals between the left and right mandibles, as well as between males and females ( P >0.05). There was no significant difference in root canal configuration between male and female ( P >0.05). In the proximal middle root, the detection rate of type Ⅳ, 2-2 was higher than that of type Ⅰ, type 1 ( P <0.05); the detection rate of type Ⅰ, type 1 was higher than that of type Ⅱ, type 2-1 ( P <0.05); the detection rate of type Ⅱ, type 2-1 was higher than that of type Ⅴ, type 1-2, type Ⅲ, type 1-2-1, type 2-1-2, and type 2-3-2 ( P <0.05). In the distal root, the detection rate of type Ⅰ, type 1 was higher than that of type Ⅳ, type 2-2 ( P <0.05), the detection rate of type Ⅳ, type 2-2 was higher than that of type Ⅱ, type 2-1 ( P <0.05). Conclusion The CBCT evaluation value of the anatomical morphology of the mandibular second molar root and root canal is high, indicating that the mandibular second permanent molar is mainly a fusion root or double root, with a high incidence of C-type root and root canal.