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This study aimed to evaluate the safety and efficacy of three-port thoracoscopic surgery for patent ductus arteriosus (PDA) ligation in children. A retrospective analysis was conducted on 50 pediatric patients with PDA (median age: 30 months; median weight: 12.00 kg; median ductal diameter: 2.50 mm) treated with three-port thoracoscopic surgery in the Department of Cardiothoracic Surgery at Kunming Children’s Hospital from January 2021 to June 2024. All 50 patients successfully underwent surgery without conversion to open thoracotomy; there was no mortality. The median hospitalization cost was 25 211.00 CNY. Postoperatively, three (6.00%) patients developed chylothorax and three (6.00%) patients had residual shunts. During the 6–36 month follow-up period, no instances of ductal recanalization or other complications were reported. In conclusion, three-port thoracoscopic PDA ligation is a safe and effective approach, offering cosmetic incisions, definitive efficacy, and low complication rates. However, meticulous handling during ductus arteriosus ligation is essential to minimize complications and residual shunts.