Considering the reward and punishment mechanism of the management committee and the complexity of innovation path selection of high-tech and general enterprises, this paper constructs an evolutionary game model of independent innovation incentive mechanism in the National Independent Innovation Demonstration Zone of China. Meanwhile, the equilibrium points of the strategy selection are solved for the three. In addition, this paper adopts numerical simulation to analyze the influence of each decision variable on different players’ strategic selections. The results show that (1) the initial willingness of the management committee, high-tech and general enterprises has different influences on each other, and these factors such as independent innovation cost, technology spillover coefficient, and patent royalty significantly affect the strategic selection of enterprises; (2) the reward and punishment mechanism of the management committee can enhance the innovation willingness of high-tech and general enterprises, in which these punitive measures can promote further the independent innovation of the two; (3) the greater the innovation subsidy provided by the management committee to high-tech enterprises, the heavier the punishment for general enterprises, and the better the effect of independent innovation incentives. The results can provide theoretical guidance and practical reference for the management committee to formulate the independent innovation incentive policies in the National Independent Innovation Demonstration Zone.