The cold/hot property of Chinese materia medica (CMM) and the application of its corresponding knowledge in the diagnosis, differentiation and treatment of diseases have been considered to be the extremely important part of traditional Chinese medicine (TCM). As highly abstracted TCM theory, the cold/hot property of CMMs is still not fully understood and remains to be elucidated by systems biology approach. The cold and hot properties of CMM are mainly defined by the response of the body to a given CMM. Metabolomics is a promising systems biology method to profile entire endogenous metabolites and monitor their fluctuations related to an exogenous stimulus. Thus, a metabolomics approach was applied to characterize the cold and hot properties of CMMs.