Under the background that China''s state-owned enterprises can only obtain lower innovation output due to their special property rights and management system, the research introduces the ambidextrous innovation under the theoretical framework of corporate governance from the perspective of system innovation and technology innovation. On this basis, the research discusses in detail how the implementation of the employee stock ownership plan of state-owned enterprises can alleviate the financing constraints faced by enterprises, and then affect the overall innovation output and ambidextrous innovation output of enterprises. At the same time, using the relevant data of China''s A-share state-owned listed companies from 2004 to 2020 for empirical testing, it is found that the implementation of the employee stock ownership plan of state-owned enterprises significantly contributes to the improvement of the overall innovation output and utilization innovation output of enterprises, but has no significant impact on the improvement of the exploratory innovation output of enterprises. The specific mechanism of the above phenomenon is consistent with the theoretical analysis, but the effect will be significantly different due to the differences in the internal characteristics of the enterprise and the design characteristics of the employee stock ownership plan. Therefore, it is suggested to actively promote the implementation of employee stock ownership plans in state-owned enterprises in various ways, especially in state-owned enterprises with high proportion of high-tech and highly educated employees, and further optimize the design of stock ownership plans, so as to better play the main role of various employees in enterprise innovation activities.