The different processes of senior executives and core technicians are used for innovation, and they are also the main incentive objects of equity incentive plans, and the interactive effect of equity incentives on innovation is worth exploring. The SME ( Small and Medium-sized Enterprise) and GEM ( Growth Enterprise Market) that successfully implemented equity incentives from 2009 to 2015 were selected as research objects, and the impact of employee equity incentives on executive equity incentives in the innovation of smes and their mechanisms were examined. The research results show that the implementation of equity incentive plans can significantly increase the quantity and quality of R&D investment and innovation output of enterprises; Compared with the senior executive equity incentive, the greater the equity incentive intensity of core technical employees, the more innovative output and the higher the quality of small and medium-sized enterprises; Executive equity incentives have a negative regulatory effect on the conversion rate of enterprise innovation. Further, the financing support effect and talent incentive effect are important mechanisms for employee equity incentive supplementation to promote innovation; The increase in R&D investment brought about by executive equity incentives cannot be regarded as a relief of the agency problem, but in essence, it is the performance result of the agency problem of the enterprise, and the agency cost plays a role in covering it.