An excess of body weight can produce morphological changes in the feet of children. The aim of this study was to assess the morphological differences of the foot in children based on their body mass index and to determine the risk factors for the development of a hallux valgus in childhood and adolescence. One Thousand Six Hundred Seventy-Eight children (5–17 years) were classified as group with obesity, overweight, and normal weight. Lengths, widths, heights and angles of both feet was measured with a 3D scanner. The risk of developing hallux valgus was calculated. Group with overweight and obesity presented longer feet (p = 0.00), wider metatarsals (p = 0.00) and wider heels (p = 0.00). Arch height was lower (p > 0.01) in the group with obesity, and the hallux angle was greater in the group with normal weight (p < 0.05). The relative risk of a lateral hallux deviation increases with age, foot length and heel width (Exp (B) > 1). Children with overweight and obesity had longer and wider feet. The arch height was higher in children with overweight, and lower in children with obesity. Age, foot length, and heel width could be risk factors for the development of hallux valgus, while metatarsal width and arch height could be protective factors. Monitorization of the development and characterization of the foot in childhood as a clinical tool could help professionals to early identify the patients presenting risk factors and prevent future deformities and other biomechanical conditions in adulthood by implementing protecting measures.