An important goal in ecology has been to reveal what enables diverse species to be maintained in natural ecosystems. A particular interaction network structure, compartments, divided subsystems with minimal linkage to other subsystems, has been emphasized as a key stabilizer of community dynamics. This concept inherently includes spatiality because communities are physically separated. Nevertheless, few theoretical studies have explicitly focused on such spatial compartmentation. Here using a meta-community model of a food web, I show that compartments have less effect on community stability than previously thought. Instead, less compartmentation of a food web can greatly increase stability, particularly when subsystems are moderately coupled by species migration. Furthermore, compartmentation has a strong destabilization effect in larger systems. The results of the present study suggest that spatial limitation of species interactions rather than of community interactions plays a key role in ecosystem maintenance.