Based on the premise that the government and high-tech enterprises are limited rationality, this study uses evolutionary game method to study the interactive mechanism between the government's supervision strategy selection and the innovation investment strategy selection of high-tech enterprises in the process of government subsidy distribution. It is found that the government's punishment for the illegal use of government subsidies by enterprises, the cost and benefit of the rational use of government subsidies by enterprises will have a direct impact the result of the game. In the unstable strategy, when the government tends to choose the strategy of "no verification", the enterprises tend to choose the strategy of "no investment" to maximize their own interests. At this time, the government of limited rationality tends to choose the strategy of "verification", and the enterprises will choose the strategy of "investment", while the government tends to choose the strategy of "no verification" again, entering a circular state, unable to reach the optimal. If we want to form a good relationship of mutual trust and mutual benefit between the government and enterprises, we will continue to have this "unable to reach optimal state " cycle. Therefore, it is necessary to add constraints to the game process.