As a key regional development strategy, regional cooperation affects the sustainable development of city-regions. This study uses social network analysis, spatial analysis, and negative binomial regression analysis to investigate the impacts of regional cooperation on green total factor productivity (GTFP) in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA). The main findings are as follows. First, regional cooperation is growing closer, unfolding a trend of networked and polycentric development patterns in the GBA. Second, the GTFP of most cities exhibits an upward trend, indicating a continuous improvement in green economic development in the GBA. Third, different types of regional cooperation have heterogeneous impacts on GTFP, with economic cooperation being essential for regional GTFP. Overall, this study provides a systematic and comprehensive analysis of the environmental effects of regional cooperation.