Against the dual strategic objectives of green-low-carbon development and innovation-driven development, a comprehensive analysis of the evolution of China’s regional green innovation ecosystems holds significant implications. Utilizing the layer by layer vertical and horizontal scatter degree method, entropy-based nonlinear programming, and a hybrid TOWA-GA operator, this study measures the development levels of green innovation ecosystems across the eight comprehensive economic zones from 2017 to 2023. The Dagum Gini coefficient and Moran’s I index are further utilized to elucidate regional disparities and spatial distribution characteristics. An obstacle degree model is adopted to diagnose critical constraining factors. Key findings reveal that: the development level of green innovation ecosystems across the eight comprehensive economic zones has risen with fluctuations, marked by pronounced regional gradients. Cross-regional overlap dominates overall variation, while intra- and inter-regional differences contribute marginally. Significant positive spatial autocorrelation emerges, with spatial linkages evolving toward homogeneous clustering supplemented by heterogeneous dispersion. Regulatory intensity constitutes the primary obstacle; shortages in financial resources, talent pools, and technological entities present additional challenges. It is suggested that differentiated and comprehensive measures should be implemented to construct a coordinated development pattern of green innovation ecosystems in the eight comprehensive economic zones.