Digital transformation gives enterprises new momentum for development. Can enterprises implementing digital transformation strategies take advantage of organizational characteristics and complex social networks to cope with the external dynamic environment to further improve the efficiency of enterprise innovation? Most of the existing studies have been conducted from the internal perspective of enterprises, and few scholars have placed the main enterprises of digital transformation in the external environment to investigate the impact of their interaction with external resources on innovation efficiency. In this context, this paper innovatively explores the mechanism of digital transformation of manufacturing enterprises on innovation efficiency from the perspective of social theory, and provides feasible suggestions for manufacturing enterprises to enhance organizational resilience and strengthen dual network embedding with the help of new generation digital information technology under the guidance of innovation efficiency. This paper takes the data of China’s A-share listed companies from 2013 to 2021 as samples for empirical analysis. The data of listed companies comes from the CSMAR database, and the patent data comes from the Wanfang database and national patent retrieval service platform. Drawing on the research methods of Wang et al. and Ahuja et al., and based on the patent application information of listed manufacturing enterprises, the cooperation network and knowledge network are constructed respectively in UCINET6.0. The empirical results show that the digital transformation of manufacturing enterprises can significantly improve the innovation efficiency of enterprises; cooperation network structure hole and knowledge network structure hole play a partial mediating role in the process of digital transformation affecting the innovation efficiency of manufacturing enterprises. The cooperation network structure hole has a stronger influence on innovation efficiency than the knowledge network structure hole. Organizational resilience positively regulates the relationship between digital transformation and dual network embeddedness in manufacturing enterprises. Heterogeneity research finds that, compared with state-owned manufacturing enterprises, non-state-owned manufacturing enterprises have a more significant improvement effect on innovation efficiency through the implementation of a digital transformation strategy. Compared with previous literature, the research significance of this paper lies in that the research conclusions can provide a social network theoretical perspective for expanding the impact mechanism of digital transformation on innovation efficiency, and provide a theoretical basis for enterprises to appropriately embed cooperation networks and knowledge networks according to practical needs to achieve sustainable development. This paper provides a path for manufacturing enterprises to improve innovation efficiency through digital transformation, and puts forward specific suggestions for manufacturing enterprises that implement digital transformation strategy to build external social networks and obtain resource information in the subsequent operation process, which reveals the internal logic of the impact of digital transformation on innovation efficiency of manufacturing enterprises to a certain extent.