Objective To explore the comparison of the clinical efficacy of thoracoscopic lobectomy and segmental pulmonary resection in the treatment of children with congenital cystic lung lesions. Methods: According to the random number table method, 103 children with congenital cystic lung lesions in our hospital from April 2022 to April 2024 were selected as the research subjects and grouped according to different surgical methods. Fifty-one cases in group A were given thoracoscopic lobectomy, and fifty-two cases in group B were given thoracoscopic pulmonary segmental resection. The surgical indicators, perioperative complications, inflammatory factors and residual lesions during the 6-month postoperative follow-up of the two groups were compared. Results: As of the last follow-up, among the 103 children, A total of 8 cases were lost to follow-up, including 4 cases in group A and 4 cases in group B. Finally, 47 cases were included in group A and 48 cases in group B. The intraoperative blood loss in group B was less than that in group A, the operation time was shorter than that in group A, and the postoperative mechanical ventilation time, thoracic drainage time, stay time in the surgical intensive care unit (SICU), and hospital stay in group B were shorter than those in group A (P<0.05). The inflammatory factor indicators in both groups increased, but those in group B were lower than those in group A (P<0.05). The incidence of perioperative complications in group B was 8.33% (4/48), which was lower than 31.91% (15/47) in the control group (P<0.05); After 6-month follow-up, there was no significant difference in the residual rate of pulmonary cystic lesions between group B (4.17%, 2/48) and group A (2.12%, 1/47) (P > 0.05). Conclusion: For children with congenital cystic lung lesions, segmentectomy can shorten the hospital stay, cause milder inflammatory responses, have fewer complications and higher safety.