The origin of variation in food chain length (FCL) has long been a central topic of ecology due to its influences on trophic control, energy flow and bioaccumulation of environmental contaminants. The positive association of FCL and ecosystem size has been consistently supported in natural systems. Recent studies, however, have begun to report no effects of ecosystem size on FCL. The emerging inconsistency among previous studies implies the existence of overlooked factors that can modulate the relationship between FCL and ecosystem size. Here, we developed a mathematical model describing metacommunity dynamics to show that large ecosystems do not necessarily support long food chains in the presence of spatially correlated disturbance. Our simple model predicted that the effect of ecosystem size was strongly dependent on the spatial extent of disturbance synchrony. When the spatial correlation of disturbance was weak, the positive association between FCL and ecosystem size appeared. However, the relationship of FCL and ecosystem size became more complex, including hump-shaped and multimodal forms, as the spatial extent of disturbance synchrony increases. This pattern emerged because larger ecosystems have wider aerial coverage, so more chances exist that an episodic disturbance hits some of the habitat patches and spreads across the landscape. Our finding highlights the important role of spatial disturbance synchrony in driving FCL, providing insights into why ecosystem size effects are variable across systems.