This paper starts from the characteristics of innovation mechanism and innovation method, combines the current situation of China's pharmaceutical industry, takes the Malerba industrial innovation system theory as the theor. support, and constructs the technol. innovation mechanism suitable for the current situation of China's pharmaceutical industry, analyzes the innovation restriction mechanism structure of pharmaceutical enterprises from the aspects of the market structure and enterprise scale of the pharmaceutical industry, technol. capital investment capacity, and innovative human capital investment capacity.From the strategic layout of pharmaceutical enterprises, the distribution of independent research and development forces, the operating mechanism that affects industry policies, the choice of pharmaceutical enterprises' technol. innovation mode, the patent system and the innovation and decision-making capabilities of pharmaceutical enterprises, the innovation operation mechanism structure of pharmaceutical enterprises are analyzed.Therefore, this article proposes measures to build a composite technol. innovation entity, broaden the ideas for improving technol. innovation capabilities, strengthen basic innovation research, highlight the ability of intellectual property to escort technol. innovation, and accelerate the incubation of technol. innovation achievements through multiple investment channels which are the key to the innovation mechanism of Chinese pharmaceutical enterprises.