Background: Sufficient knowledge of anatomy including normal patterns and aberrant variations is crucial in thoracoscopic lobectomy for congenital lung malformations (CLMs). This study aimed to investigate the prevalence of anatomical variations and their correlations with surgical outcome. Methods: Video-recordings of thoracoscopic lobectomy performed for CLMs between 2009 and 2021 were reviewed. The incidences of surgically relevant variations, including abnormal branches of pulmonary arteries and veins, aberrant systemic arteries, and incomplete fissures (as classified by Craig) were assessed in comparison with the previously published reports. Moreover, multiple univariate analyses were performed to seek correlations between surgical finding and prolonged operative times and postoperative drainage. Results: Fifty-six lobectomies were reviewed. Variations of pulmonary arteries were more commonly seen in the left lung (29.6%) compared to right (10.7%). The prevalence of atypical pulmonary venous branches was similar between the right (13.8%) and left (18.5%). The right upper oblique fissure was frequently associated with Grade 2 incomplete fissure (44.8%). Grade 3 incomplete fissure was rare (3.4%) in the right lower oblique fissure but relatively common (14.3 – 18.5%) in other locations. Grade 4 incomplete fissure was limited to the right horizontal fissure (1.7%). Multiple univariate analyses demonstrated a significant correlation between any degree of incomplete fissure and prolonged operative time (p < 0.05), whereas no factor was identified to affect need for postoperative drainage. Conclusions: The incidence of anatomical variations in CLM patients was similar to that reported in adults. Review of intra-operative video footage was useful to closely evaluate and understand anatomical variations.