The three-party evolutionary game model of government, enterprises, and institutions of higher learning is established, and the dynamic evolution process of collaborative innovation behavior is discussed under the two strategies of “incentive” and “non-incentive” chosen by the government. The results show that under the premise of stronger innovation consciousness of the government and institutions and smaller the innovation cost of enterprises, the system is easier to reach the ideal state. The incentive degree of government should be controlled within a reasonable range to prevent enterprises from falling into a bad state because of the temptation of economic interests.