In the digital era, enterprises need to explore the green development path to achieve sustainable development. Whether the digital economy can promote enterprises’ green innovation has thus become an important issue. Based on the panel data of heavy-polluting enterprises in 352 cities in China from 2015 to 2019, this article analyzes the impact of the digital economy on enterprises’ green innovation and yields three main findings: A positive relationship between the digital economy and heavy-polluting enterprises’ green innovation is confirmed and accompanied by the lag effect. Mechanism analysis indicates that absorption capacity plays an important mediating role in this process. Further, the hypothesis concerning the U-shaped relationship is proved empirically, indicating that heavy-polluting enterprises’ green innovation can be improved under the digital economy shocks but with a specific level context. This article suggests that the government should pay attention to the digital economy development, and encourage enterprises to increase investment in scientific research. This research provides empirical evidence for the effectiveness of applying the digital economy in advancing green innovation in China’s heavy-polluting enterprises.