Resolving the conflict between economic growth and ecological sustainability is crucial when transitioning from traditional economic development towards a sustainable green model. In this context, the super-NSBM model was applied to measure the efficiency of green innovation technology research and development. Additionally, it was applied to measure the efficiency of the green innovation achievement transformation among 30 Chinese provinces. This evaluation was conducted for the period from 2011 to 2021, and it utilized a two-stage innovation value chain perspective. The entropy method was used to comprehensively calculate the digital economy development index, and the impact of digital economy development on the two-stage green innovation effect was empirically explored using SDM. The findings revealed the following: Firstly, both two-stage green innovation efficiency and digital economy development exhibited significant spatial characteristics. Secondly, digital economy development had a positive effect on two-stage green innovation efficiency not only in the local region but also in neighboring regions. This conclusion remained valid throughout a series of robustness tests. Thirdly, in terms of regional heterogeneity, the eastern region and non-resource-based regions had greater digital economy development dividends than the central, western, and resource-based regions; therefore, the effect on two-stage green innovation efficiency was more significant. Lastly, both intellectual property protection and data factor endowment exerted positive moderating effects on the influence of the digital economy on two-stage green innovation efficiency. The conclusions of this research provide a theoretical backing for and empirical proof of the mechanism of digital economy development and its impact on two-stage green innovation efficiency. Policy implications are suggested based on these findings, such as reinforcing digitalization, establishing targeted policies, and fostering a favorable external environment conducive to technological innovation.