Dune systems can have alternative stable states that coexist under certain environmental conditions: a vegetated, stabilized state and a bare active state. This behavior implies the possibility of abrupt transitions from one state to another in response to gradual environmental change. Here, we synthesize stratigraphic records covering 12,000 years of dynamics of this system at 144 localities across three dune fields in northern China. We find side-by-side coexistence of active and stabilized states, and occasional sharp shifts in time between those contrasting states. Those shifts occur asynchronously despite the fact that the entire landscape has been subject to the same gradual changes in monsoon rainfall and other conditions. At larger scale, the spatial heterogeneity in dune dynamics averages out to produce relatively smooth change. However, our results do show different paths of recovery and collapse of vegetation at system-wide scales, implying that hysteretic behavior occurs in spatially extended systems.