Congenital lung malformations (CLM) are most commonly treated with a pulmonary lobectomy. However, due to technological advancement, video-assisted thoracoscopic surgery (VATS) segmentectomy is becoming an attractive alternative to VATS lobectomy. This study aimed to evaluate the safety, feasibility, and efficacy of VATS segmentectomy as a lung parenchyma-saving strategy in children with CLM. A retrospective analysis was performed on 85 children, for whom VATS segmentectomy was tried for CLM between January 2010 and July 2020. We compared the surgical outcomes of VATS segmentectomy with the outcomes of 465 patients who underwent VATS lobectomy. Eighty-four patients received VATS segmentectomy and thoracotomy conversion was necessary for one patient for CLM. The mean age was 3.2 ± 2.5 (range 1.2–11.6) years. The mean operative time was 91.4 ± 35.6 (range 40–200) minutes. The median duration of chest tube drainage was 1 (range 1–21) day, and the median length of postoperative hospital stay was 4 (range 3–23) days. There were no postoperative mortality and postoperative complications developed in 7 patients (8.2%), including persistent air leakage in 6 patients (7.1%) and postoperative pneumonia in 1 patient (1.2%). The median follow-up period was 33.5 (interquartile range 31–57) months and there were no patients requiring re-intervention or reoperation during the follow-up period. In the VATS segmentectomy group, the persistent air leakage rate was higher than in the VATS lobectomy group (7.1 vs. 1.1%,p= 0.003). Otherwise, postoperative outcomes were comparable between the two groups. VATS segmentectomy in children with CLM is a technically feasible alternative to VATS lobectomy with acceptable early and mid-term outcomes. However, the persistent air-leakage rate was higher in VATS segmentectomy.