Strengthening disruptive scientific and technological innovation is an important foundation for accelerating the high-level scientific and technological self-reliance. Considering the differences in the paths of different government R&D subsidy policies to encourage disruptive scientific and technological innovation, by constructing a game model between the government, scientific research institutions and science and technology enterprises, the decision-making logic and path mechanism of all parties to promote the output of disruptive scientific and technological innovation achievements are discussed, and Matlab 2021a is used for simulation analysis, Finally, a collaborative governance path to promote disruptive scientific and technological innovation achievements is obtained.