Objective To summarize the surgical treatment experience in neonates with coarctation of the aorta (CoA) and aortic arch hypoplasia (AAH). Methods The neonates with CoA and AAH who underwent surgical treatment in the Department of Pediatric Cardiac Surgery of Guangdong Provincial People's Hospital from 2013 to 2020 were retrospectively enrolled. The postoperative complications, long-term survival rate, and freedom from aortic reobstruction were analyzed. Patients undergoing extended end-to-end anastomosis were allocated into an extended end-to-end group, those undergoing extended end-to-side anastomosis into an extended end-to-side group, and those undergoing pulmonary autograft patch aortoplasty into a patch aortoplasty group.Results Finally 44 patients were enrolled, including 37 males and 7 females, aged 5.00-30.00 (19.34±7.61) days and weighted 2.00-4.50 (3.30±0.60) kg. There were 19 patients of extended end-to-end anastomosis, 19 patients of extended end-to-side anastomosis, and 6 patients of pulmonary autograft patch aortoplasty. The mean values of the Z scores of the proximal, distal, and isthmus of the aortic arch were –2.91±1.52, –3.40±1.30, and –4.04±1.98, respectively. The mean follow-up time was 45.6±3.7 months. There were 2 early deaths and no late deaths. Aortic reobstruction occurred in 8 patients, and 3 patients underwent reoperation intervention. The 5-year rate of freedom from reobstruction was 78.8%. The Cox multivariable regression analysis showed that the related factors for postoperative reobstruction were the Z score of the preoperative proximal aortic arch (HR=0.152, 95%CI 0.038-0.601, P=0.007) and the postoperative left main bronchus compression (HR=15.261, 95%CI 1.104-210.978, P=0.042). Conclusion Three surgical procedures for neonates with CoA and AAH are safe and effective, but the aortic reobstruction rate in long term is not low. The smaller Z score of the preoperative proximal aortic arch and the postoperative left main bronchus compression are risk factors for long-term aortic reobstruction.