Blue Carbon Ecotones (BCEs) play a critical role in regulating abiotic and biotic ecological fluxes underpinning services which are also critical for protection in the land-ocean continuum. Previous assessments of BCEs typically focused on specific aspects such as fishery, carbon storage, or biodiversity. The sustainable conservation and development of BCEs at the global and local scale requires a comprehensive assessment of their systemic health status and its drivers to control. Here, we proposed a novel Benefit-Pressure-Transformation Risk model (BPT model) to calculate Ecotone Health Index (EHI) for mangrove, salt marsh, and seagrass as core BCEs, based on habitat structure, species morphological features, ecological services, pressures from both nature and human activities, vulnerability of species, and niche overlap. The health status of BCEs is more sensitive to structural indicators such as area, fragmentation, and height compared to co-dependent environmental pressure. For instance, 54% and 13% of mangroves' EHI are explained by species height and marine pressure, respectively. Thus, the focus on BCE's structure, where connectivity plays a dominant role in habitat and species integrity, is critical for enhancing EHI. This research provides clear analytics along coastlines at a pixel resolution of 1 °(lat)
× 1 °(long)(100km × 100km at the equator) globally with a novel index EHI, and yet setting a quantitative basis for BCEs assessment. Our BPT model is not just a descriptive framework, but a flexible tool that can be applied to all ecosystems at any scale.