Due to persistent technological impacts on ecological efficiency (eco-efficiency) and variations in economic power and resource endowments among regions, considering regional and temporal heterogeneity becomes imperative. Ecosystems, often divided into economic production and environmental governance stages, necessitate a holistic assessment incorporating regional, temporal heterogeneity and stage distinctions. To address potential issues of a technology gap ratio (TGR) exceeding 1 within a two-stage network structure with dual heterogeneity, we introduce a segmented projection three-layer meta-frontier analysis method. In empirical study, we systematically examined eco-efficiency, emissions inefficiency and technology gaps across management, regional and temporal dimensions in 30 Chinese provinces from 2016 to 2020. Findings reveal disparities in management eco-efficiency, with the central provinces outperforming the east. Regional differences indicate advanced technology in the east, contributing to superior eco-efficiency. Temporal analysis highlights the positive role of scientific and technological development. Emissions inefficiency improvements are noted, necessitating attention toward management and regional technology levels. Eastern provinces exhibit superior emissions efficiency, emphasizing the role of regional and technological development. Recommendations include prioritizing environmental governance, strengthening regional collaborations and implementing policies to bridge technology gaps.