Abstract Background To compare the clinical outcomes between thoracoscopic approach and thoracotomy surgery in patients with Gross type C Esophageal atresia (EA) and tracheoesophageal fistula (TEF). Methods Patients with Gross type C EA/TEF who underwent surgery from January 2007 to January 2020 at Beijing Children’s Hospital were retrospectively analyzed. The patients were divided into two groups according to surgical approaches. The perioperative factors and postoperative complications were compared among the two groups. Results One hundred and ninety patients (132 boys and 58 girls) with a median birth weight of 2975 (2600, 3200) g were included. The primary operations were performed via thoracoscopic (n = 62) and thoracotomy (n = 128) approach. After comparison of clinical characteristics between the two groups, we found that there were statistically significant differences in associated anomalies, method of fistula closure, duration of mechanical ventilation after surgery, feeding option before discharge, management of pneumothorax, and prognosis (all P 0.05). Conclusions Thoracoscopy surgery for Gross type C EA/TEF is a safe and effective, minimally invasive technique with comparable operative time and incidence of postoperative complications.