Based on the endogenous perspective, with the data of high tech enterprises in small and medium sized A share sectors from 2009 to 2017 as the research sample, this paper uses the value added capital rate to measure the enterprise performance and constructs a simultaneous equations model to empirically analyses the impact of R&D investment, managerial compensation incentives and equity incentives on the performance of high tech enterprises. The results show that the there is an inverted U shaped relationship between salary incentive and R&D investment or enterprise performance. There is a positive correlation between equity incentive and enterprise performance, and an inverted U shaped relationship between salary incentive and R&D investment. R&D investment has a negative impact on current enterprise performance, while its lagging effect on enterprise performance is positive. Further research finds that the above conclusions are common in private enterprises, but not obvious in state owned enterprises.