The impact of digital empowerment on green innovation is increasingly evident, enabling various subjects to improve the integration of innovation elements and enhance innovation efficacy across a broader temporal and spatial scope. A comprehensive examination of the mechanisms that underlie this process is required. This paper constructs the ‘elements-subjects-environments’ research framework of digital innovation ecosystems, collecting data from 30 provinces in China from 2017 to 2021 and using green total factor productivity (GTFP) to evaluate the level of green regional development. In this study, the dynamic qualitative comparative analysis (QCA) method is employed to analyze the intricate causal mechanisms and configurations of green regional development that are driven by digital innovation ecosystems from both temporal and spatial perspectives. The results show that: (1) green regional development requires the interaction of multiple elements, subjects, and the environment, and a single condition does not constitute a necessary condition; (2) there are four pathways with different configurations for high-level green development: data elements-driven enterprise application innovation, data elements-driven enterprise-user co-creation, data elements-driven multi-collaborative innovation, and digital environment-driven university basic innovation; (3) the temporal and spatial dimensions of China’s green regional development pathways are heterogeneous: the significance of data elements in fostering green regional development is increasing; the multi-collaborative innovation configuration is facilitating the green development of the eastern and central regions, whereas the western and northeastern regions are progressing at a relatively slow pace. This study provides theoretical and practical insights to promote the integration of digital innovation and green development.