<p>Ecosystems face amplified variability and abrupt reorganization under climate and land-use change, yet the role of vertical vegetation structure over millennia remains poorly constrained. Here we show, using Holocene pollen, charcoal, palaeoclimate and human-activity proxies from the Eastern China Monsoon Region, how tree, shrub and herb layers relate to ecosystem variability and potential tipping points. Shrubs are associated with reduced variability in northern temperate forest–grassland mosaics and southern subtropical forests, consistent with buffering that maintains continuity between canopy and ground layers. In the more open warm-temperate central region, shrub buffering is weak and lower variability depends mainly on a woody framework. Potential tipping points are asynchronous, with earlier transitions in the structurally weaker central region. As transitions are approached, shrubs shift from buffering variability to being linked with vegetation reorganization under intensifying fire, climatic stress and human activity. These results identify shrub-mediated vertical coupling as a key axis of long-term ecosystem stability.</p>