This study aimed to determine the relationship between individual and combined phthalate metabolites and body composition in children and adolescents using data from the 2015-2018 National Health and Nutrition Examination Survey. Single-exposure analysis indicated that most phthalate metabolites were negatively correlated with areal bone mineral density (aBMD). Quantile g-computation demonstrated a negative relationship between the mixture of phthalate metabolites and aBMD, which was confirmed by the Bayesian kernel machine regression model. Sex-stratified analysis revealed that mono-butyl phthalate (MBP) was negatively correlated with aBMD, and MBP, mono-ethyl phthalate (MEP), and mono-isobutyl phthalate (MiBP) were negatively linked to lean mass in males but not in females. The results did not differ according to developmental stages (childhood vs. adolescence). Our findings indicate that phthalate metabolites may affect the body composition in children and adolescents, particularly aBMD. Certain phthalate metabolites seem to be sex-specific, with males showing higher sensitivity than females.