Traditional Chinese Medicines (TCMs) are evidenced to confer therapeutic actions by largely interacting with dysregulated multi-layers molecules that underlie diseases,which can be defined as the holistic characteristics of TCMs to treat different diseases.The fact is that systems biology,and metabolomics have the robust-capacity to better understand the holistic characteristics by globally deciphering the complex interactions between TCMs and diseases associated with dysregulated molecules.Currently,they are widely used to address many key questions in TCMs involving chemical characterization,therapeutic efficacy,toxicology and metabolic features,etc.