<p>Thoracoscopic anatomical lesion resection (TALR) and lobectomy (TL) are the main surgical procedures for congenital lung malformations (CLMs). Single-center studies suggest that TALR preserves healthy lung tissue better than TL, but its generalizability across diverse clinical settings remains unverified. This multicenter retrospective cohort study aims to compare TALR and TL in children with CLMs, focusing on postoperative outcomes, recurrence rates, and lung function preservation. The retrospective, multicenter, observational study, with 6 hospital in China already involved. Pediatric patients (aged &lt; 14 years) with a diagnosed CLMs between January 2020 and December 2024 after surgery will be eligible for inclusion. The outcomes will include demographics, clinical characteristics, therapeutic strategies and postoperative outcomes. These will be compared using mixed-effects models and the Student’s t-test, non-parametric test or χ² test. Propensity score matching will be used to ensure an even distribution of known confounders between the groups. The collaborating hospitals obtained local approval based on a standard ethics application from internal ethics committees or acknowledged an existent ethics approval of the leading institution with approval from internal ethics committees. Due to the retrospective nature, written informed consent from patients was waived by the ethics committee. The results will be published in academic journals and presented at national and international academic conferences. As the largest comparative study of minimally invasive CLM resection techniques in children, this protocol addresses critical knowledge gaps in surgical decision-making. Results will provide evidence-based guidance for selecting lung parenchyma-sparing strategies that optimize postoperative outcomes while maintaining safety. </p>