Under the background of the increasingly close connection between innovation activities and financing activities, the characteristics and attributes of capital have become an important factor in building a high-level cycle of “technology, industry and finance”. From a theoretical perspective, this article analyzes the impact and internal mechanisms of equity and debt, which have long-term guidance and governance roles, on the innovation efficiency of manufacturing enterprises under the framework of “patient capital”. It proposes that “patience” refers to long-term cooperation relationships and supervisory governance roles, while “efficiency” represents the effective utilization of innovation resources. The two are compatible, which means that long-term orientation can promote efficiency improvement. At the empirical level, based on data from A-share listed manufacturing companies from 2011 to 2022, the research findings are as follows. Firstly, patient capital effectively promotes the enhancement of innovation efficiency in manufacturing enterprises, with relational debt exhibiting a more pronounced promotional effect. In comparison to constructive innovation, patient capital is more conducive to promoting high-value and high-risk modular innovation. Secondly, patient capital can alleviate information asymmetry and mitigate principal-agent conflicts, thereby further enhancing the innovation efficiency of manufacturing enterprises. Thirdly, the digital economy plays a positive role in facilitating the improvement of innovation efficiency in manufacturing enterprises through patient capital. Specifically, the improvement of urban digital economy significantly enhances the promotional effect of relational debt, while the enhancement of corporate digital transformation is more conducive to strengthening the promotional effect of strategic equity. Finally, patient capital is more effective in promoting the improvement of innovation efficiency in manufacturing enterprises with weaker market power, as well as those in the growth and maturity stages. Based on the research findings, the policy recommendations are as follows. We should actively cultivate patient capital and fully leverage its advantages in reducing information friction and optimizing corporate governance, comprehensively develop the digital economy to provide favorable conditions and effective tools for patient capital to participate in the innovation governance of manufacturing enterprises, and guide the effective matching of different types of patient capital with manufacturing enterprises at different stages of development and facing different market structures.