Childhood obesity has been shown to be closely related to future obesity and comorbidities. As its prevalence and impact has increased significantly worldwide, researchers have focused on prevention and intervention. This study assessed a multifaceted intervention for elementary school children.A retrospective data collection with a cohort analysis was employed. A 16-week school-based intervention with nutritional intervention, physical activity, and behavioral education was designed and conducted by a multidisciplinary team for 1860 children aged 6 to 13 years. Basic information, anthropometrics, and physical fitness (PF) were recorded before and after the intervention. The differences compared with a reference group, and compared between subgroups, were analyzed.Significant favorable changes in body weight and composition were found. Children's height, weight, and muscle weight increased, whereas BMI, BMI z-score (zBMI), waist circumference, hip circumference, waist-hip ratio, waist-height ratio, body fat percentage, and visceral fat area decreased. Sit-ups and 800-m run time significantly improved. Girls exhibited a greater reduction in body weight outcomes; boys improved more in body composition and PF. Students with higher zBMI had a greater reduction in all anthropometrics; students with lower zBMI showed greater PF improvement, except for the 800-m run.The intervention improved weight measures, body composition, and PF. Subgroup differences suggested the need for sex- and weight-specific interventions.