The effectiveness of the innovation incentive policies has been widely concerned. From the New Institutional Perspective，we discuss the influence of the external environment characteristics of the enterprises on the effectiveness of tax incentives, and point out that the enterprises in the strong institutional environment may be rewarded by the initiative to meet external requirements rather than to improve internal efficiency. Using the panel data of 2009-2013, through empirical research, we find that tax incentives, to some extent, improve the enterprise's innovation performance, in which innovation investment played a complete intermediary role. However, there are differences between different enterprises. Politically connected enterprises did not put the savings into innovative activities effectively. However, they also have received a considerable amount of tax discount. As a result, high tech enterprise income tax preferential policies are more likely to be the “tax shield” for these enterprises. The research results of this paper have a certain reference value to the improvement of the tax incentives policies of high tech enterprises in China.