Objective: To describe the different pathological characteristics of congenital basilar invaginations and discuss the surgical treatment of such cases. Methods: A total of 139 patients diagnosed with basilar invaginations underwent surgical treatment from 2008 to 2015. Based on Atul Goel’s classification and simultaneous consideration of atlantoaxial dislocation or syringomyelia,the cases were subdivided into four groups. Individualized posterior surgical decompression and/or atlantoaxial reset procedures were performed to correct atlantoaxial dislocation,decompress the brain stem,or resolve syringomyelia. The indications and critical points of each procedure were documented. Results: All 139 patients were surgically treated; 27 patients(19.4%) had underwent at least one decompression surgery previously. On an average,there was gratifying clinical improvement based on the Japanese Orthopaedic Association score analysis.One patient exhibited severe post-operative infection,and the fusion instrument was removed. One patient experienced fracture of internal fixation. Two patients exhibited persistent respiratory symptoms at early stages after the surgery. Four patients felt worse at the latest follow-up. There was no surgical mortality. The poor outcome/morbidity in this series was 5.8%(8/139). Conclusion: The different pathological image characteristics of congenital basilar invaginations based on the presence or absence of syringomyelia and/or atlantoaxial dislocation,reflected the pathological features of complicated basilar invaginations more accurately. Based on these features,different posterior decompression and/or reset procedures,combined with occipitocervical fusion and C1-2 fusion,could be tailored to different patients. These individualized surgeries could reduce surgical complications,decrease morbidity and mortality,and further promote positive outcomes.