The mechanism of Chinese medications have some characteristic such as multi-pathway, multi-components, multi-targets and so on, which decide the direction of systems research. In the recent years, microarrays be concerned with the relative field of Chinese medications for its superiority of highthough, parallel and high-density. This paper mainly generalize the approach of these methods in the recent three years, such as finding effective target of Chinese medications, effective part of Chinese medications, checkup of Chinese medications, screening new drugs and so on. We suggest the concept of Pharmacogenomics of Chinese medications with the guidance of the theory of Chinese medications for further development of Chinese medications.