Energy theory of drug and cooperation mechanism of energy for active ingredients of Chi-nese materia medica (CMM) were put forward. Concepts of "correlation energy of disease" and "synthetic Chinese formulated medicine" were given- The third way: "simplicitycomplexity" for modernization of CMM was proposed. Science theory in Chinese formulated medicine was discussed by cooperation mecha-nism of energy for active ingredients which suggested that CMM be indispensable for recovery of some dis-eases. With the aid of computing chemistry, molecular simulation, biology informatics and pharma-cokinetics, it is possible to investigate and confirm correlation energy of different diseases and combina-tions of active ingredients of Chinese formulated medicines. Problems of different producing areas, confu-sions of species and instability of CMM quality can be solved by returning from chemical synthetic drug to synthesize the Chinese formulated medicine.