Objective To provide the basis for endoscopic craniocervical junction surgery through cervical CT image and endoscopic odontoid process anatomy of atlas, axis and odontoid.   Methods A total of 150 cases of cervical vertebrae were selected for high resolution thin slice plain CT measurement to evaluate the atlantoaxial structure and its adjacent structure, and to estimate the safe boundary of odontoid process resection. The atlantoaxial odontoid process was anatomized on 3 cadaver head specimens under endoscope through the submandibular approach using STORZ endoscopy system and endoscopic surgical instruments.  Results The average length of atlas anterior arch and other anatomical marks were measured by CT, and the safety boundary area of odontoidectomy was estimated to be (240.9 ± 39.92)mm2, male: (248.3 ± 49.64)mm2, Female: (233.2 ± 24.54)mm2. Through the submandibular endoscopic approach, the atlantoaxial anatomy and odontoidectomy anatomy made a transverse incision at the midpoint of the connecting line between one mandibular angle and hyoid bone to expose the submandibular triangle area. Under the endoscope, the digastric muscle and the greater angle of hyoid bone were exposed through the submandibular triangle area, and the retropharyngeal space was passively separated layer by layer to the prevertebral space to expose the prevertebral fascia. After removing the prevertebral tissue, the atlas, the dentate process of the axis, the atlantooccipital joint, the atlantoaxial joint, and part of the foramen magnum were fully exposed.  Conclusion Estimating odontoid resection safety boundary area by CT image, in combination with endoscopic odontoidectomy anatomy via sunbmandibular approach, we can perform the surgery safely and efficiently under the bright of endoscope with surgical instruments, which can significantly reduce the incidence of cerebrospinal fluid leakage and postoperative infection while decompressing.