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Manufacturing industry is the lifeblood of national economy, and innovation input is the lifeline of manufacturing enterprises. This paper selects the financial data of China’s listed manufacturing companies from 2015 to 2019 to study the moderating effect of governance structure on the relationship between innovation input and firm performance. It is found that innovation investment has a negative influence on firm performance with lag. In terms of ownership structure, ownership concentration has a negative moderating effect on the relationship between innovation input and firm performance. The degree of equity balance has a positive moderating effect on the relationship between innovation input and firm performance. According to the conclusion of this study, it is expected to optimize the governance structure of China’s manufacturing enterprises and promote industrial development.