Previous studies have suggested that the global ocean density stratification below approximate to 3000m is approximately set by its direct connection to the Southern Ocean surface density, which in turn is constrained by the atmosphere. Here the role of Southern Ocean surface forcing in glacial-interglacial stratification changes is investigated using a comprehensive climate model and an idealized conceptual model. Southern Ocean surface forcing is found to control the global deep ocean stratification up to approximate to 2000m, which is much shallower than previously thought and contrary to the expectation that the North Atlantic surface forcing should strongly influence the ocean at intermediate depths. We show that this is due to the approximately fixed surface freshwater fluxes, rather than a fixed surface density distribution in the Southern Ocean as was previously assumed. These results suggest that Southern Ocean surface freshwater forcing controls glacial-interglacial stratification changes in much of the deep ocean.