Government-industry-university-institute collaboration innovation is the great motivation to implement the innovation-driven strategy, promote development of national and regional economics. However, there are some drawbacks in the mechanism of collaborative innovation of industry-university-institute that is led by industry, such as the weakened effect of government-leading, the low motivation and efficiency of colleges and universities which participate in it. According to these shortages, the government is viewed as the main body of collaboration innovation and then the tripartite evolutionary game model about collaboration innovation, which is guided by government, is led by university and is with the participation of industry, is constructed. In order to figure out the game evolution strategies of government, industry and university in different situation, the strategy choices among the government, industry and university during the collaborative innovation process are analyzed. Providing the collaboration innovation center constructed by Jiangsu Province as a case, the factors that influence the strategy choices of government-industry-university-institute collaboration innovation are studied by simulation. The result reveals that the influence degree of government, industry and university's willingness is different from each other. The enterprises' behavior to participate in collaboration innovation is mostly likely to be influenced by the market behaviors. Instead, the colleges' behavior to attend collaboration innovation are more likely to be influenced by the willingness of government, and the enterprises are more sensitive to the college's willingness. Different government motivation mechanisms affect the enterprises and university respectively. The policy support of government is more attractive to the enterprises, and the financial support impacts the universities more. Moreover, the enterprise is more sensitive to the penalty and the income distribution. The enterprise takes the profit maximization as the goal, while the colleges aim at the scientific research achievement and developing the talents. And also the change of the penalty and interest distribution affects the enterprise behavior choices more. In this article, the government is taken as the behavior main body to analyze the collaboration innovation game with the enterprise and the college. And the study provides the reference significance to the tripartite evolutionary game model of government-industry-university-institute.