Purpose: The aim of this study was to investigate the clinical effectiveness of azygos vein preservation when using a thoracoscope in the operation for type III esophageal atresia for children. Materials and Methods: We retrospectively analyzed the clinical data of 34 patients (group B) who underwent the thoracoscopic operation of type III esophageal atresia with azygos vein preservation from January 2017 to April 2018. The clinical data of 36 patients (group A) who underwent the thoracoscopic operation of type III esophageal atresia with azygos vein mutilation from April 2015 to December 2016 were selected as a control group. Results: All patients were successfully operated on. There was no significant difference in the operation time, amount of bleeding, mechanical ventilation time, and intensive care time between the azygos vein mutilation group and azygos vein preservation group. Compared with the operation severing the azygos vein, preservation of azygos vein has obvious advantages in postoperative hospitalization time, the incidence of anastomotic leakage (P < .05). The follow-up results for 1 year after the operation showed that the incidence of anastomotic stricture with preservation of azygos vein was significantly lower than that with azygos vein transection (P < .05). Conclusions: The thoracoscopic operation of type III esophageal atresia with azygos vein preservation can not only improve the edema of esophageal tissue around the esophagus, but also reduce the occurrence of esophageal anastomotic leakage and accelerate the postoperative recovery of children, and it has the same safety as the operation with azygos vein mutilation.