According to the recent report, there are 870 million people suffer from ocular diseases worldwide. The present approaches for diagnosis are morphological examination, imaging examination and immunological examination, regrettably, they lack of sensitivity and difficult to make a definite diagnosis in the early stage. Systemic biology as an effective method has been used in clinical diagnosis and treatment for diseases, especially metabolomics which is more attractive with high sensitivity and accuracy. Although previous researches had been confirmed that endogenous metabolites in the ocular matrix play a crucial role in the progress of diseases related diseases, the standard protocols and systematic summary about the biomarker researches based on ocular matrix has not been established. This review article highlights the pretreatment for ocular matrix and the new biomarkers expressed by the eye diseases, expected to promote the application of biomarkers in the diagnosis and treatment of eye diseases.