Taking the 2010—2015 listed companies in GEM as a sample, we use panel data and its robustness standard mis-correction model to discuss the relationship of governance structure, R&D investment and corporate performance. The results show that:state-owned shareholding negatively influences the R&D investment, the balance ownership structure positively influences the R&D investment, the ownership concentration and managerial shareholding both have the nonlinear relationship with R&D investment; The “convergence of interest effects” and the “entrenchment effects”, based on the executive incentive, moderating the role of government subsidies; R&D activity has a significant hysteresis effect, which negatively affects the current corporate performance, however, it also has a significant positive effect on the two-stage lag performance. Optimizing the corporate governance structure and solving the agency problem from the root cause is the basic path to improve the efficiency of R&D activity and promote the steady development of enterprises.