Background and Aims Thromboangiitis obliterans (TAO) is an organic disease affecting small and medium-sized arteries and veins in the extremities. Its cause is unknown, and treatment options are limited. With advances in medical technology, the most commonly used methods are great saphenous vein arterialization surgery and endovascular surgery. However, there is no consensus on the superiority of these two procedures. Therefore, this study was performed to compare the clinical efficacy of great saphenous vein arterialization surgery and endovascular surgery in treating TAO, aiming to provide a reference for clinical treatment.Methods The clinical and follow-up data of 183 patients diagnosed with TAO at the First Affiliated Hospital of Xinjiang Medical University from January 2015 to April 2023 were retrospectively analyzed. Among them, 40 patients underwent great saphenous vein arterialization (great saphenous vein arterialization group), and 143 patients underwent endovascular treatment (endovascular treatment group). The patients were matched 1:1 based on age (±5 years) and TASC classification of the lesion segment, resulting in 36 pairs of patients, all male. Relevant clinical indicators were compared between the two groups.Results There were no statistically significant differences in the baseline data between the two groups after matching (all P>0.05). The great saphenous vein arterialization group showed better postoperative patency rates and ankle-brachial index than the endovascular treatment group and a lower rate of secondary surgical interventions (all P<0.05). The endovascular treatment group had better outcomes regarding postoperative pain visual analogue scale scores, intermittent claudication, and length of hospital stay, than the great saphenous vein arterialization group (all P<0.05). The two groups had no significant differences regarding postoperative foot coldness/numbness, gangrene, amputation rates, and postoperative infection (all P>0.05). Kaplan-Meier curve analysis indicated that the long-term prognosis was better in the great saphenous vein arterialization group (P<0.05).Conclusion Compared to endovascular treatment, great saphenous vein arterialization surgery is more effective in treating TAO, offering higher patency rates and lower secondary surgical intervention rates, lower costs, and better mid-to-long-term efficacy. For patients with financial difficulties, great saphenous vein arterialization surgery may be a choice to improve mid-to-long-term outcomes. Although endovascular treatment provides better short-term clinical efficacy, such as relief from resting pain, its long-term prognosis is less favorable than great saphenous vein arterialization surgery. Therefore, without suitable vascular grafts, endovascular surgery is optional to reduce postoperative pain and improve the patient's quality of life.