Purpose <p>To investigate the clinical application of stay sutures in thoracoscopic repair for esophageal atresia (EA) combined with tracheoesophageal fistula (TEF).</p> Methods <p>A total of 56 neonates diagnosed with Type C EA received thoracoscopic correction surgery from May 2019 to December 2024. The patients were divided into 2 groups randomly: (1) Esophageal anastomosis was constructed using interrupted sutures on the posterior wall and continuous locked stitches on the anterior wall assisted by two stay sutures (Group A; <i>n</i> = 30) and (2) Esophageal anastomosis was performed using traditional techniques with interrupted sutures on both anterior and posterior walls (Group B; <i>n</i> = 26). A comprehensive comparison of operative parameters and postoperative complications was systematically conducted between the two surgical methods.</p> Results <p>The mean anastomotic time was significantly shorter in Group A (20.5 ± 3.3&#xa0;min) compared with Group B (41.0 ± 4.5&#xa0;min, <i>P</i> &lt; 0.05). Similarly, operation time was 126.5 ± 15.5&#xa0;min in Group A versus 154.5 ± 13.5&#xa0;min in Group B (<i>P</i> &lt; 0.05). Postoperative ventilator support duration was 2.1 ± 0.7&#xa0;days in Group A versus 2.3 ± 0.6&#xa0;days in Group B (<i>P</i> &gt; 0.05). The time to first oral intake was 8.5 ± 1.8&#xa0;days in Group A versus 9.3 ± 3.2&#xa0;days in Group B (<i>P</i> &gt; 0.05). An upper gastrointestinal series performed on postoperative day 5–7 revealed anastomotic leakage in 4 of 30 patients (13.3%) in Group A versus 6 of 26 patients (23.1%) in Group B (<i>P</i> &gt; 0.05). Anastomotic stenosis was observed in 6 patients (20%) in Group A and 6 patients (23.1%) in Group B postoperatively, also with no statistically significant difference between the groups (<i>P</i> &gt; 0.05). No recurrence of TEF was observed in each group.</p> Conclusion <p>This innovative approach significantly shortens the operative time in the thoracoscopic treatment of Type C EA.</p>