To summarize the variation types of the axis in patients with basilar invagination (BI), then propose a classification scheme of the axis deformity. From December 2013 to September 2020, 92 patients (male 42, female 50) who were diagnosed with BI were studied retrospectively. Based on the imaging data of CT, the width and height of the axis pedicle and the sagittal diameter of the lateral mass were measured in each patient. According to the development of axis pedicle and lateral mass, the types of axis variation were summarized, and then the classification scheme of axis deformity was put forward. All cases were analyzed and axis deformities were divided into four types. Type I: the axis is basically normal (53 cases, 57.6%). Type II: axis lateral mass is dysplasia (eight cases, 8.7%), which includes two subtypes: type IIA, the axis unilateral lateral mass is dysplasia (three cases); type IIB, the axis bilateral lateral masses are all dysplasia (five cases). Type III: axis pedicle is dysplasia (11 cases, 12%), which is subdivided into two subtypes: type IIIA, the axis unilateral pedicle is dysplasia (six cases); type IIIB, the axis bilateral pedicles are all dysplasia (five cases). Type IV: axis pedicle and lateral mass are all dysplasia (20 cases, 21.7%), this type contains the following four subtypes: type IVA, the unilateral axis pedicle and unilateral lateral mass (contralateral or ipsilateral) are all hypoplasia (four cases); type IVB, the unilateral axis pedicle and bilateral lateral masses are all hypoplasia (five cases); type IVC, the bilateral axis pedicles and unilateral lateral mass are all dysplasia (seven cases); type IVD, the bilateral axis pedicles and bilateral lateral masses are all dysplasia (four cases). The left and right abnormal lateral mass sagittal diameter (Type II) was (7.23 ± 1.39) mm and (5.96 ± 1.37) mm, respectively, the left and right abnormal pedicle width (Type III) was (2.61 ± 1.01) mm and (3.23 ± 0.66) mm, respectively, left and right abnormal pedicle height (Type III) was (5.43 ± 2.19) mm and (4.92 ± 1.76) mm, respectively. Moreover, the classification scheme has good repeatability and credibility. The classification about axis deformity could provide personalized guidance for axis screw placement in the BI and other upper cervical surgery, and axis screw placement errors would be effectively avoided.