Metabonomics is a new branch in the omics-field following the development of genomics, transcriptomics and proteomics, with its research object being the collection of metabolites-metabolome and the downstream products of life. Metabonomics is a new method to study on the metabolic network and the relationship between body and environment, which conforms to the basic theory, diagnosis and treatment of traditional Chinese medicine (TCM), and provides powerful technical support in the modern study of TCM. This paper is to review the application of metabonomics in the research on the mechanism of TCM prescription injections, syndrome study and safety evaluation and consistency evaluation of TCM injections.