This study aims to elucidate the metabolic differences between obese adolescents categorized into low-weight-loss (LWL) and high-weight-loss (HWL) groups. The objective of this study is to investigate the metabolic characteristics of obese adolescents, with a focus on the statistically significant individual differences observed in weight loss outcomes after the same dietary and exercise training intervention. A four-week exercise and dietary intervention was administered to the participants. Obese adolescents were categorized into LWL (with a weight loss percentage of 5-10%) and HWL (with a weight loss percentage of >10%) groups on the basis of their weight loss outcomes. Post-intervention changes in body morphology and body composition between the two groups were compared using Analysis of Covariance (ANCOVA), with gender as a covariate. Additionally, metabolic changes were analyzed in depth; differential metabolites between the groups were identified through ANCOVA adjusted for gender, followed by pathway analysis. After the four-week exercise intervention, the body morphology and composition of the obese adolescents showed significant improvements compared with those before the intervention ( < 0.001). For example, weight decreased from 80.65 kg to 72.35 kg, BMI decreased from 30.57 kg/m to 27.26 kg/m, waist circumference decreased from 103.64 cm to 94.72 cm, and body fat percentage decreased from 32.68% to 28.54%. Prior to the exercise intervention, no significant differences in body morphology and composition were observed between the HWL and LWL groups ( > 0.05). After the intervention, the HWL group demonstrated significant improvements in weight, body mass index, waist circumference, body fat percentage, fat mass, fat-free mass, body water amount, and skeletal muscle mass compared with the LWL group ( < 0.001). After controlling for the levels of pre-intervention metabolites, 27 differential metabolites were identified between the HWL and LWL groups. These metabolites were categorized into fatty acids, amino acids, organic acids, carnitines, indoles, benzoic acids, and carbohydrates. Notably, they were significantly enriched in the eight metabolic pathways involved in amino acid metabolism, fatty acid biosynthesis, and coenzyme A biosynthesis. A four-week exercise intervention enhanced the body morphology and physical fitness of obese adolescents, although the degree of weight loss varied among individuals. Considerable weight reduction was significantly correlated with metabolites involved in lipid, amino acid, organic acid, carbohydrate, and gut microbiota metabolism and with the enrichment of pathways involved in amino acid metabolism, fatty acid biosynthesis, and coenzyme A biosynthesis. These findings indicate that intrinsic metabolic characteristics considerably influence individual responsiveness to exercise-based weight-loss interventions.