Backgrounds <p>This research aims to characterize the metabolic profiles of prepubertal patients with TS to elucidate the potential impact of X chromosome haploinsufficiency on glycolipid metabolism.</p> Methods <p>Fouty-nine prepuberty TS and 50 age-, sex- and BMI standard deviations scores (SDS)-matched healthy children (HC) were enrolled. Untargeted ultra-performance liquid chromatography–coupled mass spectroscopy was performed in all participants. Differentially expressed metabolites (DEMs) were identified and annotated using the KEGG and HMDB databases. Correlation analyses were conducted to explore associations between DEMs and relevant clinical parameters. Logistic regression models were performed to evaluate the potential impact of the interaction between X-chromosome haploinsufficiency and metabolite abnormalities on metabolic status.</p> Results <p>Metabolomics analyses indicated separation between TS and HC groups with 70 DEMs enriched in caffeine metabolism, purine metabolism, and insulin resistance pathways. Among TS, 34 DEMs were found to be correlated with height, weight, glucose and lipid metabolism, and sex hormone levels. Three DEMs-sodium cholate, N-arachidonoyl-L-serine, and N1-pyrazin-2-yl-4-chlorobenzamide--were identified to interact with X chromosome haploinsufficiency in influencing metabolic status.</p> Conclusions <p>Prepubertal children with TS exhibit distinct metabolic profiles, with DEMs enriched in caffeine metabolism, purine metabolism, and insulin resistance pathways. These metabolites show correlations with clinical parameters and demonstrate interactions with X chromosome haploinsufficiency affecting metabolic health.</p> Impact <p><UnorderedList Mark="Bullet"> <ItemContent> <p>This study described the distinctive metabolic profiles of TS children for the first time.</p> </ItemContent> <ItemContent> <p>The impact of X chromosome haploinsufficiency on glycolipid metabolism was elucidated through a study of prepubertal TS children.</p> </ItemContent> <ItemContent> <p>Three novel metabolites were identified with significant interaction effects with X chromosome haploinsufficiency on glycolipid metabolic status.</p> </ItemContent> </UnorderedList></p>