Studying the essence of a syndrome has been a key challenge in the field of Chinese medicine. Until now, due to limitations of the methods available, the progress towards understanding such complicated systems has been slow. Metabonomics encompasses the dynamics, composition and analysis of metabolites, enabling the observation of changes in the metabolic network of the human body associated with disease. Being from the point of view of the whole organism, metabonomics provides an opportunity to study the essence of a syndrome to an unprecedented level. Phlegm and blood stasis syndrome is the main syndrome associated with coronary heart disease (CHD), which bring difficulties in clinical treatment due to difficulties associated with differentiation of symptoms and signs. The fundamental differences of material between the two also need to be interpreted. The authors consider that we can use the method of combining a disease (in this case CHD) with associated syndromes (phlegm and blood stasis syndrome) to select patients with phlegm and blood stasis syndrome of CHD, and utilize metabonomics to explore the essence of the syndrome by difference analysis of metabolite spectra. Meanwhile, we can study the syndrome in CM, observe the change regularity of metabolism spectra after the treatment of corresponding and non-corresponding prescription and syndrome, in order to validate the material fundament in the progress of syndrome formation and their differences. This will not only have great significance in enhancing the ability to identify syndrome of phlegm and blood stasis in CHD and to establish the clinical curative criteria, but will also offer a new approach of studying the essence for a syndrome using metabonomics.