Abstract:Collaborative Innovation is the country’s innovative plan in the new period which follows the development of times and has important strategic significance. Based on the experience of Cooperative Innovation, this paper found that collaborative innovation achievements are facing with three kinds of risks through the investigation: publishing academic papers which leads to the research results become public knowledge; incomplete cooperation agreements resulting in research results becoming private property; weak protection of the collaborative innovation center, which leads to the research results are stolen. Preventing and controlling the above-mentioned risks mainly should do as the followings: (1)reforming colleges’ single scientific research evaluation system; (2)strengthening the completeness of cooperation agreement; (3)improving and implementing the system of "one prize and two rewards "; (4)improving the internal management mechanism of the cooperative innovation center; and (5) strengthening the protection consciousness of intellectual property.