Objective Transnasal endoscopic nasopharyngectomy is currently the optimal choice of minimally invasive surgery for nasopharyngeal skull base lesions, but internal carotid artery (ICA) injury is a potential risk of this surgery. This study aims to evaluate the course of ICA and its spatial relationship with related structures through preoperative multiple dimensional observation and three-dimensional image reconstruction of computed tomography (CT) data of patients, so as to guide nasal endoscopic nasopharyngeal and parapharyngeal skull base surgery. Methods Head enhanced CT data of 40 cases (80 sides) without pathological manifestations of nasopharynx and its surrounding skull base were selected. The relationships between ICA and surrounding bone structures in different layers were measured on the image workstation, and the spatial relationships between ICA and surrounding structures were observed by three-dimensional reconstruction of the images. Results On the plane of the bony inferior turbinate, the distances from the posterior margins of the bony inferior turbinate (PMBIT)， posterior margins medial pterygoid plate(PMMP)， posterior margins lateral pterygoid plate(PMLP), midline to the ICA were (38.8±4.0) mm, (25.9±2.8) mm, (19.7±3.8) mm, (23.8±2.7) mm, respectively. The angles between the line PMBIT-ICA and the PMBIT elongation, the line PMMP-ICA and the PMMP elongation were (15.0±4.0)° and (17.0±6.0)°, respectively. On the plane of the inferior choanae, the distance from the PMMP to the ICA was (27.2±3.5) mm, the angle between the line PMMP-ICA and the PMMP elongation was (12.0±4.0)°. The three-dimensional reconstruction obtained clear stereoscopic images. Course variation occurred in 40% of the extracranial part of the ICA, most of which were tortuosity type, located at the level of oropharynx to pharyngeal recess and protruding to the posterior pharyngeal wall. Conclusions Individualized preoperative three-dimensional CT reconstruction can provide key anatomic information for transnasal endoscopic nasopharyngeal skull base surgery, facilitate intraoperative localization of ICA, and improve surgical safety. The extracranial part of ICA has a high variation rate, protrudates to the posterior pharyngeal wall with increased risk of endoscopic nasopharyngeal-parapharyngeal skull base surgery, which should be adequately evaluated before surgery.