Confronted with an escalating ecological crisis, regional cooperation has emerged as a recognized strategy for orchestrating collective actions among diverse stakeholders across territories. Nonetheless, the potential of regional cooperation in mitigating ecological footprints remains significantly underexplored. To address this gap, this study employs the case of the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) to quantitatively scrutinize the impacts of regional cooperation on ecological footprints from 2010 to 2018, while also elucidating its underlying mechanisms. Our investigation into the GBA unveils four pivotal findings. First, the data paints an increasing ecological footprint picture across the GBA, with a discernible spatial pattern of decreasing intensity from coastal to hinterland cities over the past decade. Second, intergovernmental cooperation amplifies the ecological footprint, a phenomenon intricately tied to top-down interventions from upper-level governments. Such highly formalized spatial interventions often overlook local ecological repercussions, thereby intensifying discord. Third, the collaboration between government and market entities aids in reducing the ecological footprint, provided it is contingent on the symbiotic relationship between regional market competition policies provided by the upper-level government and the flexible, informal arrangements offered by local governments to support enterprises. Last, regional cooperation may intensify the ecological footprint in ordinary cities through the transfer of industries from core cities.