Chinese drug R&D and industrial development has entered a leap-forward stage of innovation. More and more pharmaceutical enterprises cooperate with universities, scientific Research institutions, CRO (Contract Research Organization) contract outsourcing service agencies for R&D. Each link of cooperative research is faced with great risks. Combined with the process of innovative drug research and development, the organization and cooperation of each link were identified, and the risks faced by Chinese pharmaceutical enterprises were analyzed. Based on the Rasmussen social system hierarchy model, a 5-level risk framework for cooperative R&D of innovative drugs was established. Through the case analysis of Beigene cooperative R&D project, the Accimap model of cooperative R&D risk was constructed, and the influence path of the factors among the levels of risk of cooperative R&D of innovative drugs in China was clarified with the combination of information flow transmission channels. Based on the PSR(Pressure-State-Response) model, the countermeasures and suggestions are put forward according to the risks of our innovative drug cooperative R&D.