More detailed knowledge of root and canal morphology is important in order to improve the success in the endodontics of primary teeth. The purpose of this study was to evaluate the root and canal morphology of primary mandibular second molars (PMSMs) in a Chinese population using cone-beam computed tomography (CBCT). Methods: CBCT images, which had been obtained previously in the West China Hospital of Stomatology at Sichuan University, Chengdu, China between May 2009 and December 2011, were screened retrospectively. Finally, 283 individuals—207 male and 76 female with a mean age of 7.2 years (range 3–10 years)—and 487 PMSMs with clear images of root and canal morphology were enrolled. The number of roots and morphology of canals were recorded. The patient's gender, and the symmetry and frequency of three roots in PMSMs were analyzed. Results: The majority of PMSMs had two (72.28%) or three roots (27.52%). The symmetrical incidence of three-root PMSMs in this Chinese population was 50.65%. There is no difference between genders in the prevalence of an extra root and the incidence of symmetry (p > 0.05). Of the individuals enrolled, 25.26% of PMSMs had three canals and 73.31% had four canals. The root canal systems of the PMSMs in the present study were categorized into seven variants. Conclusion: This study indicated that three-rooted PMSMs occur frequently in the Chinese population. There was no difference between the two genders on incidence and symmetry. The majority of PMSMs have three to four canals and the diversity of the root canal variants should be considered when performing clinical procedures. CBCT is a good option for studying the root and canal morphology of primary teeth.