Innovation is an important driving force for economic growth. At the critical stage of the transition from "Made in China" to "Intelligent Manufacturing in China", enterprises must rely on innovation to strengthen their core competitiveness in order to obtain more profits. Executives are the key decision makers of an enterprise and have an important influence on the innovation activities of the enterprise. The article uses the panel data of 949 listed companies in China from 2010 to 2017. First, the panel fixed effects model and the panel negative binomial regression model are used to empirically test the impact of executive compensation incentives on corporate R&D investment and R&D output. The results show that the three modes of executive compensation incentives, namely monetary compensation, equity and on-the-job consumption incentives, have significantly promoted corporate innovation activities. Secondly, this article also explores the heterogeneous impact of executive compensation incentives on corporate innovation activities. On the one hand, the sample enterprises are divided into subsample groups of state-owned and non-state-owned enterprises according to the nature of their ownership. We find that compared with state-owned enterprises, executive compensation incentives significantly promote the innovative activities of non-state-owned enterprises. On the other hand, the sample enterprises are divided into high-tech enterprises and non-high-tech enterprise subsample groups according to their industry categories. We find that the equity incentive model significantly increased the R&D investment of high-tech enterprises and the R&D output of non-high-tech enterprises. In order to test the reliability of the above empirical results, this paper also uses the measurement method of replacing the R&D investment and R&D output indicators of enterprises to conduct a robustness test. The results show that the significant positive correlation between executive compensation incentives and enterprise R&D innovation is still stable. Considering the factors such as the degree of risk aversion and personal ability of the executives will not only affect the level of executive compensation, but also affect the decision-making of the executives on corporate innovation. This paper takes the policy event of "2014 central enterprise compensation reform" as the midpoint of time, constructs a quasi-natural experiment, and uses a double difference model to empirically test the impact of the exogenous policy impact of the 2014 central enterprise compensation system reform on corporate innovation. The results show that the executive compensation control policy has significantly reduced the R&D investment of state-owned enterprises, but the impact on its R&D output is not significant. Therefore, this article puts forward the following policy recommendations:First, to stimulate the enthusiasm of enterprise executives for active innovation, we should design executive compensation incentive contracts that combine explicit and implicit incentives, and appropriately introduce non-short-term accounting performance indicators in the management evaluation plan. Second, to encourage innovative behaviors of enterprises, we should improve the compensation incentive mechanism for state-owned enterprise executives by means of "unification of the two powers" and long-term equity incentives. Third, the application of on-the-job consumption incentives in high-tech enterprises can be appropriately improved, supplemented by auditing supervision and control so as to avoid the occurrence of executive opportunistic behavior.