Basilar invagination has been classified into two types by Goel: Type A is defined mechanical instability of the atlantoaxial joint with upward displacement of the odontoid process while Type B is characterized by stable atlantoaxial joints. This study reviews the association between radiological features and symptomatology and prognosis of two types of basilar invagination for better clinical management. A retrospective analysis was conducted including 141 patients diagnosed with basilar invagination who underwent surgical treatment from January 2016 to December 2020. The neurological function was assessed by the JOA scores, and Short-Form 12 scores. Logistic univariate and multivariate analyses were performed to predict prognostic risk factors. Type A patients (21/101, 20.8%) with more cases of dizziness, lower preoperative JOA scores and SF-12 PCS scores (JOA, 13.0 vs. 13.9, P = 0.042; SF-12 PCS, 37.48 vs. 38.42, P = 0.034) compared to type B (2/40, 5%) (P = 0.022). Type B (22/40, 55%) with more cases of ataxia than type A (35/101, 34.7%) (P = 0.026). Patients with type B demonstrated a significantly higher improvement rate in SF-12 PCS than type A (P = 0.018). Further logistic regression revealed that onset age >= 45 years (OR 4.654, 95% CI 1.645-13.165; p = 0.004) and basal angle >= 125 degrees (OR 28.139, 95% CI 1.090-726.239; p = 0.044) were independent risk factors for type A and type B, respectively. Type A patients with more cases of dizziness, and type B patients with more cases of ataxia, can achieve better long-term prognosis following clinical intervention.