Operationalizing the planetary boundaries (PB) framework at a regional scale is a critical sustainability challenge. This study addresses this gap within the Yangtze River Economic Belt (YREB), a globally significant nexus of urban, agricultural, and ecological systems. By integrating 30 m land use data with socioeconomic statistics, we developed an improved ecosystem service value ( \({V}_{E}\) ) calculation method and coupled ecological carrying capacity (EC) with ecological footprint (EF) to establish an ecological boundary (EB) model. Our findings reveal three key insights: (1) Total ESV increased by 92.4%, with forests and water bodies contributing 83.6%, forming a spatial differentiation pattern centered on the Yangtze mainstream; (2) Additionally, significant differences in ecological boundary values were observed, with eastern regions exhibiting values 2.3–4.8 times higher than those in the west; (3) Geodetector analysis identified per capita GDP, R&D intensity, and urbanization rate as key drivers of ecological boundary transgressions. This research validates the application of downscaled planetary boundaries for robust ecological governance and introduces a holistic framework for “boundary delineation–mechanism deconstruction–policy coordination” tailored to regional ecological conditions.. This research provides two primary contributions. Scientifically, it pioneers a robust methodology for regionalizing the PB framework, offering a new paradigm for assessing socio-ecological systems. Practically, it provides an evidence-based blueprint for a differentiated, interregional governance strategy, advocating for technological compensation from the east to support targeted ecological conservation in the west. This offers a scalable model for reconciling development with resilience in critical river basins globally.