Eco-hydrological zoning is a key challenge in eco-hydrology. Large-scale principal component and clustering fail to capture eco-hydrological coupling or support adaptive management. Multiscale eco-hydrological zoning enables refined, coordinated regional management of ecosystems and water resources. Taking the Yarlung Zangbo River Basin as an example, we quantified the eco-hydrological index (EHI) through entropy and catastrophe progression methods and divided into three eco-hydrological zones: a low-water, a normal-water and a multi-water from 2000 to 2020 integration of five scales, and analyzed drivers of zones with the Optimal Parameters-based Geographical Detector (OPGD) and Partial Least Squares-Structural Equation Modeling (SEM). The results showed that (1) the low-water zone aligned with sandy land, bare rock, and permanent ice/snow; the normal-water zone correlated with alpine grasslands and the multi-water zone matched alpine wetlands and forests. (2) Over the 20-year period, eco-hydrological zoning pattern overall remained stable, normal-water ecological zone averaged 56.98 %, the low-water and the multi-water ecological zones averaged 18.15 % and 24.87 %, increased 0.18 % and 0.39 %. (3) GDP and vegetation cover were the primary driving factors influencing EHI with the interactions between driving factors primarily characterized by double-factor enhancement, and synergistic effects between drivers substantially exceed their individual contributions. (4) Ecological and topographic factors were positively correlated with EHI, while human activities, climate and hydrology factors were negatively correlated with EHI. Topography indirectly influenced EHI by shaping climate and affecting human activities. The eco-hydrological zoning of Nature reserves and Ecological red lines offers direction for the protection, monitoring, and ecological restoration of protected areas.