To discuss the current situation of Chinese materia medica industry and put forward tactics for the construction of innovation system based on the theory of national innovational system. Now there are several problems in the innovation system of Chinese materia medica industry, such as the lack of resource, the ambiguity between the subject and object, achievments in scientific research being hardly transformed to products, and the ignorance of training personnel, etc. These problems should be solved by taking measures so as to establish the innovation system of Chinese materia medica industry as soon as possible and make great efforts on the subject, the platform, the qualified personnel resource, and the institution of the innovation system.