Endometriosis (EMS), a chronic estrogen-dependent inflammatory disorder, affects 0.7%-8.6% of women in the general population and 9.0%-68.0% of those with subfertility, making it a leading cause of secondary infertility. Despite its significant clinical burden, EMS remains challenging to diagnose early in a noninvasive manner through conventional methods, with diagnostic delay averaging 8.6 years. Advances in detection technologies and bioinformatics have enabled metabolomics to serve as a powerful tool for biomarker discovery and mechanistic investigation of disease pathogenesis. Metabolomics analyses have identified multiple metabolic abnormalities in EMS patients, including dysregulation of carbohydrate, lipid, and amino acid metabolism, providing novel insights into disease mechanisms. This review comprehensively examines recent metabolomics research related to EMS pathophysiology, clinical features, staging, noninvasive diagnostics, therapeutic strategies, and risk factors, while critically evaluating methodological limitations. We highlight the clinical translational potential of metabolomics technology and multi-omics integration approaches, offering new perspectives to advance mechanistic understanding of EMS, facilitate development of early noninvasive diagnostic methods, and identify novel therapeutic targets.