Building a digital government is an important measure to achieve modernization of the national governance system and governance capacity. A quasi natural experiment based on the reform of big data governance institutions, using empirical data from A-share listed companies in Shanghai and Shenzhen stock markets from 2015 to 2022 as samples, constructed an interleaved DID model to empirically test the impact and mechanism of government digital transformation on enterprise innovation. Research has found that government digital transformation significantly promotes corporate innovation, manifested in a comprehensive increase in R&D investment and patent output. The analysis of the impact mechanism found that government digital transformation can help enterprises innovate by promoting enterprise digital transformation and the development of digital finance. Further analysis reveals that the government's digital transformation has promoted exploratory innovation in enterprises and improved patent quality. Heterogeneity analysis found that the impact of government digital transformation on enterprise innovation is more significant in samples of high-tech enterprises and low levels of regional digital infrastructure improvement. The research conclusion helps to further clarify the microeconomic effects of government digital transformation from the perspective of enterprise innovation, and has important implications for improving innovation incentives and regulatory policies in the era of big data, and promoting the national strategy of innovation.