Objective To compare the application of cuffed and uncuffed endotracheal tubes in full‑term neonates undergoing congenital intestinal atresia surgery. Methods Sixty newborns who were scheduled to perform congenital intestinal atresia surgery under general anesthesia were selected. They were divided into two groups, according to the random number table method (n=30): a cuffed endotracheal tube group (group C) and an uncuffed endotracheal tube group (group U). Group C used cuffed endotracheal tubes for surgical procedures, while uncuffed endotracheal tubes were adopted in group U. Both groups were compared for the changing rate of endotracheal tubes and airway condition after surgery [the incidence of hypoxemia within 5 min after extubation (SpO2<95%), laryngospasm and post-operative wheezing], and the incidence of inspiratory pneumonia during follow‑up visit one week after surgery. Results Patients in group U presented increases in the changing rate of endotracheal tubes (26.7% vs 3.3%), the incidence of hypoxemia within 5 min after extubation (10.0% vs 0), laryngospasm incidence (10.0% vs 0) and inspiratory pneumonia incidence (10.0% vs 0), compared with those in group C (P<0.05). There were no statistical difference in the incidence of post-operative wheezing between the two groups (P>0.05). Conclusions Cuffed endotracheal tubes are superior to uncuffed ones in full‑term neonates during congenital intestinal atresia surgery, with good efficacy. Postextubateion stridor) after extubation were observed between the two groups. Results The rate of re-intubation in U group was significantly higher than C group(P＜0.05) .Infants suffered from airway secretions as hypoxemia , laryngospasm after extubation in U group,were higher than that in C group. and the episodes of postextubateion stridor didn,t happen among the two groups , The incidence rate of aspiration pneumonitis in C group was lower than U group(P＜0.05).Conclusion Compared with uncuffed endotracheal, cuffed endotracheal may be more suitable in full-term neonates during the operation of congenital intestinal atresia, the usage was satisfactory and feasibility.