To study the incidence of congenital posterior arch defects of the atlas and in combination with other congenital variations in the Chinese population. 1405 images of cervical three-dimensional computed tomography (3D CT) and 1284 images of head and cervical three-dimensional computed tomography angiography (3D CTA) were retrospectively reviewed, including images of 1539 males and 1150 females. These images of cervical 3D CT and head and cervical 3D CTA were obtained in the Department of Radiology of two hospitals, Second and Third People's Hospital of Jingzhou, China, from January 2020 to October 2023. And congenital posterior arch defects of the atlas were classified according to the criteria of Currarino et al. Congenital posterior arch defects of the atlas combined with other congenital variations including occipitalization of the atlas, the ponticulus posticus variation of the vertebral artery groove of the atlas, cervical fusion, and the transversal foramen of the atlas variant were also observed. A total of 2689 subjects were included in this study. The overall prevalence of congenital posterior arch defects of the atlas was 0.74% (20/2689). There was no statistically significant difference in incidence between males (0.78%,12/1539) and females (0.70%,8/1150) (P >0.05). Among all posterior defects, type A and B defects were found in 0.6% (16/2689) and 0.15% (4/2689) cases, respectively. There were no type C, D, and E defects and no anterior arch defects. But in 20 cases of congenital posterior arch defects of atlas, 40%(8/20) combined with other congenital variations including occipitalization of atlas in 4 type A cases, bilateral complete ponticus posticus variation of atlas vertebral groove in one type A case, C2-3 fusion in one type A case, coexistence of unilateral complete ponticulus posticus variation of the vertebral artery groove of the atlas and unilateral unclosed transverse foramen in one type B case, and coexistence of unilateral unclosed transverse foramen in one type A case. The incidence of congenital posterior arch defects of the atlas was low in Chinese population. There was no difference between males and females. Type A and B were the two major defects in Chinese population, and the prevalence of type A and B combined with other congenital cervical variations were higher than those of type C, D, and E.