Digital finance can revolutionize the financial system and bridge the gap between urbanization and green innovation. This study provides novel insights into how digital finance influences regional green innovation disparities in China, using panel data from 284 prefectures (2011-2020). The findings indicate that (1) regional green innovation experiences a “Matthew effect” of digital finance, with notable variations in structure. This conclusion is robust to instrumental variable and difference-in-differences tests. The “Matthew effect” shows a dynamic superposition effect with a diminishing marginal effect in the time dimension. (2) Mechanism analysis suggests that while digital finance weakens the “Matthew effect” by reducing financing restrictions and capital mismatch, it widens the regional green innovation gap by promoting market demand, innovation, and entrepreneurial vigor. (3) Heterogeneity analysis shows that the “Matthew effect” of digital finance on the green innovation gap is more evident in cities with weak commercial charm. (4) Effective governance, including entrepreneurship, intellectual property protection, and financial regulation, is crucial for mitigating the “Matthew effect.” This study provides insights into the complex relationship between digital finance and regional green innovation disparities, offering valuable implications for policymakers seeking to foster the harmonious development of regional green innovation.