Constipation in children is a common functional gastrointestinal disorder that seriously affects quality of life and physical and mental health. Traditional research methods have limitations, making it difficult to fully elucidate the complex etiology and individual variability of constipation. In recent years, metabolomics, as an important branch of systems biology, has been widely applied to the study of pediatric constipation by systematic analysis of various metabolites. This review summarizes the application of metabolomics technologies in pediatric constipation research, focusing on characteristic changes in metabolite profiles and regulatory mechanisms of related metabolic pathways in children with constipation, and evaluates potential pathogenic mechanisms and therapeutic targets. It aims to provide a theoretical basis for individualized treatment of pediatric constipation and to point out future research directions.