Introduction Based on the representative data reflecting the level of physical development and athletic quality, such as the “National Physical Health Test for Students”, it is shown that the physical health status of adolescents and children in China is decreasing annually, and the trend of obesity is gradually increasing. Objective Analyze and study the effect of training on the physical fitness of obese children aged 12 to 14 through school soccer training. Methods The effect of school soccer training on the health and physical fitness of obese children aged 12-14 years was studied, and conclusions were drawn by the literature method, experimental method, mathematical statistical method, and logical analysis method. Forty-eight screened obese children were randomly assigned to the experimental and control groups, 24 in each group. The experimental group underwent 12 weeks of soccer training, and the control group underwent 12 weeks of no training control. The subjects’ body composition and flexibility quality indices were measured post-intervention. Results The visceral fat index, body fat rate, and muscle rate of boys and girls progressed expressively, with a significant difference (P <0.05). Muscle weight is also known as lean body weight, with an expressive increase in muscle tone. In comparison, the increase in fat weight and muscle ratio in boys was expressively higher than in girls. Conclusion Regular long-term school soccer training can increase mobility in obese children, increase physical flexibility, and help promote physical health and prevent injury. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.