Abstract objectives: We aimed to report the prevalence of anatomic variations in Chinese pediatric patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and to explore the correlation between anatomic variations and the extent of chronic sinusitis in children. Design: This retrospective study conducted between January 2018 and June 2020. Setting:This study involved children from the First Affiliated Hospital, Sun Yat-sen University and Guangzhou Women and Children’s Medical Center. Participants: Participants included 50 children with CRSwNP. Main outcome measures: The diagnosis of CRSwNP was based on symptoms, endoscopy, and computed tomography examination according to European criteria on chronic rhinosinusitis. The presence of anatomical variations was determined, and its correlation with disease extension was analyzed. Results: Fifty children were included in the study. The anterior ethmoid sinus was the most commonly affected sinus in children, followed by the maxillary, posterior ethmoid, frontal, and sphenoid sinuses. Agger nasi cells were the most common anatomic variation in children sinus (96%), followed by inferior turbinate hypertrophy (60%), septal deviation (55.1%), concha bullosa (45.8%), Onodi cells (44.9%), Haller cells (38%), and paradoxical middle turbinate (4%). No significant correlation was found between anatomic variation and corresponding sinusitis hypertrophy and maxillary sinusitis (P > 0.05). Conclusions: Our results found no correlation between anatomic variations and sinusitis in pediatric CRSwNP. The occurrence of pediatric CRSwNP is as attributed more to immunological, infectious, or other factors rather than anatomic variations.