Objective: To explore the remodeling effect of a 12 week supervised exercise intervention on the relative proportion of body composition among junior and senior high school students with obesity using compositional data analysis (CoDA), to clarify the longitudinal association between body composition changes and the improvement of metabolic syndrome (MetS), and to identify the core body composition targets for ameliorating metabolic risk in adolescents. Methods: A randomized controlled trial design was employed in March 2025. Totally 182 obese adolescents aged 12-18 years from two junior and senior high schools in Tianjin were recruited and randomly assigned to an exercise intervention group ( n =92) and a health education control group ( n =90) at a 1∶1 ratio. The intervention group received a 12 week supervised aerobic combined with resistance exercise intervention (4 sessions/week, 60 min/session), while the control group only received routine health education concurrently. Body composition was determined using 3.0 T magnetic resonance imaging. With students sex specific MetS Z score as the core outcome, compositional data were processed via isometric log ratio transformation. Statistical tests were performed combining repeated measures MANOVA, multiple linear regression, and analysis of covariance. Results: After the intervention, the overall body composition of the intervention group changed significantly ( F =18.72, P <0.01), with the relative proportion of visceral fat decreasing the most (change the isometric logratio: -0.17), and the betweengroup difference was statistically significant ( P <0.01). The relative mass of visceral fat before and after the intervention was positively correlated with the MetS Z score (before intervention: β =1.02, 95% CI =0.06-1.98; after intervention: β =1.42, 95% CI =0.58-2.26, both P <0.05), and there was no statistically significant difference in the slopes and intercepts of the regression models between the two time points (both P >0.05). When the magnitude of weight loss was fixed, a greater relative reduction in visceral fat was associated with a more significant decrease in the MetS Z score. Conclusions The relative proportion of visceral fat is a core stable marker for MetS risk in obese junior and senior high school students. A 12 week supervised combined exercise intervention can effectively reduce the proportion of visceral fat and improve the risk of metabolic syndrome among junior and senior high school students.