This review discusses the application of metabolomics in clinical biomarker discovery and therapeutic target identification. Metabolomics, which involves the systematic analysis of small-molecule metabolites, is crucial for understanding disease mechanisms and identifying potential therapeutic targets. Mass spectrometry-based metabolomics is a key technique for analyzing changes in endogenous metabolites and their associated metabolic pathways in biological samples. It has been widely used in various fields, including the analysis of herbal compounds and the identification of biomarkers for disease diagnosis, prognosis, and treatment evaluation. The review highlights the importance of metabolomics in revealing the metabolic signatures of diseases and identifying potential therapeutic targets. It also discusses the use of metabolomics in the discovery of biomarkers for various diseases, including cancer, diabetes, and neurodegenerative disorders. The review emphasizes the role of metabolomics in understanding the metabolic pathways involved in disease progression and in the development of new therapeutic strategies. The application of metabolomics in the study of herbal medicine and natural products is also discussed, highlighting its potential in the discovery of new drugs and therapeutic targets. The review concludes that metabolomics is a powerful tool for the discovery of biomarkers and therapeutic targets, and its integration with other technologies is essential for advancing the understanding of disease mechanisms and the development of new treatments.This review discusses the application of metabolomics in clinical biomarker discovery and therapeutic target identification. Metabolomics, which involves the systematic analysis of small-molecule metabolites, is crucial for understanding disease mechanisms and identifying potential therapeutic targets. Mass spectrometry-based metabolomics is a key technique for analyzing changes in endogenous metabolites and their associated metabolic pathways in biological samples. It has been widely used in various fields, including the analysis of herbal compounds and the identification of biomarkers for disease diagnosis, prognosis, and treatment evaluation. The review highlights the importance of metabolomics in revealing the metabolic signatures of diseases and identifying potential therapeutic targets. It also discusses the use of metabolomics in the discovery of biomarkers for various diseases, including cancer, diabetes, and neurodegenerative disorders. The review emphasizes the role of metabolomics in understanding the metabolic pathways involved in disease progression and in the development of new therapeutic strategies. The application of metabolomics in the study of herbal medicine and natural products is also discussed, highlighting its potential in the discovery of new drugs and therapeutic targets. The review concludes that metabolomics is a powerful tool for the discovery of biomarkers and therapeutic targets, and its integration with other technologies is essential for advancing the understanding of disease mechanisms and the development of new treatments.