The aim of this study was to investigate the anatomical factors influencing the incidence of accessory canals (ACs) in the apical third of the mandibular second molar in Chinese population.Micro-CT was performed on 86 root canals. The five possible factors influencing the incidence of ACs in the apical third were named X1 to X5. These factors were the canal length of the apical third, fused roots, location of apical foramen, curvature of the root canals, and complexity of the canals. Statistical analysis was performed by the least absolute shrinkage and selection operator, receiver operating characteristic curve, and the χ2 test (α = 0.05).The selected variables in the least absolute shrinkage and selection operator regression model were fused roots and complex root canals. The area under the curve was 0.737, indicating that the model had a certain predictive ability. ACs were mainly distributed in the buccal wall and mesial wall of root canals in the apical third of molars (p < 0.05).For Chinese population, fused roots and complex root canals are anatomical factors influencing ACs in the apical one-third of mandibular second molars, and the ACs mainly occur in the buccal wall and mesial wall of the root canal.