Based on the systematic analysis of the development trend of the digital economy and regional structure, we focused on the heterogeneous influence mechanism of digital economy development on regional green innovation quality. The research finds that, on the whole, the development of the digital economy has a significant promoting effect on the improvement of regional green innovation quality. Interestingly, with the improvement of the development level of the digital economy, there are differences in its driving mechanisms for the quality of regional green innovation. A lesser level of digital economy development is not conducive to improving the quality of regional green innovation. But when digital economy development rises, it can positively drive the quality of regional green innovation. Once the level of digital economy development breaks through the critical scale. In other words, the higher the level of inter-regional digital economy development, the more beneficial it is to promote the quality of green innovation.