Abstract: Metabonomics is a new discipline defined as the qualitative and quantitative measurement of low-molecular-weight metabolites in organisms subject to pathophysiological stimuli or genetic modification. This method enables us to have a new perspective on metabolic variation. It provides the possibility of exploring the biomarkers of diseases for early diagnosis and pathogenesis of diseases. The research techniques used in metabonomics include nuclear magnetic resonance (NMR) technique and mass spectrometry (MS). The unsupervised method and supervised method are useful statistical techniques for the analysis of metabonomic data. In this article, the application of metabolomics in clinical diagnosis and drug toxicology are reviewed briefly with an emphasis laid on its progress in ophthalmology. We focused on the research progress of metabolomics in early diagnosis, differential diagnosis, pathogenesis and drug efficacy of particularly relevance to eye diseases such as ocular trauma, uveitis, cataracts, ocular hypertension and optic neuropathy.