Objective To develop a 3D visualization endoscopic navigation system based on CT portal angiography (CTPA) and explore its clinical value in assisting precise treatment of esophageal and gastric varices (EGV). Methods Patients with EGV needing treatment in the Department of Gastroenterology of Zhongshan Hospital, Fudan University from September 2021 to April 2023 were collected. Preoperative examinations including CTPA and hematological examinations were performed, and a 3D visualization endoscopic navigation system was developed to assist endoscopic treatment. Real time comparison was made between the endoscopic 3D portal vein system image reconstructed by intelligent imaging and the actual endoscopic observation of the vascular morphology inside the cavity. The responsible blood vessels that are prone to bleeding were embolized using a sandwich injection method of “lauromacrogol+tissue adhesive+lauromacrogol”. For patients with portal shunting, ultrasound-guided coil insertion was performed. Postoperative endoscopic ultrasound or CTPA was used reexamination to evaluate vascular embolism and complications. Results A total of 13 patients successfully underwent endoscopic ultrasound-guided variceal embolization. The average maximum inner diameter of target veins was (3.3\begin{document}$ \pm $\end{document}1.3) cm; on average, implanted coil number was 1(0,2) in each patient, with median dosages of lauromacrogol and tissue adhesive were 9.5(7.8,10.0) mL and 1.5(1.0,2.1) mL respectively. Postoperatively, endoscopic ultrasound detecting confirmed complete occlusion of all target veins. At 8 weeks after treatment, none of the patients experienced rebleeding. At 24 weeks after treatment, rebleeding occurred in 3 patients, on postoperative days 107, 126 and 147, respectively. Conclusion The 3D visualization endoscopic navigation system based on CTPA can effectively and safely assist preoperative diagnosis and intraoperative localization of target blood vessels, which is beneficial for the precise treatment of EGV patients.