Intense debate persists about the timing and magnitude of the wet phases in the East Asia deserts since the late Pleistocene. Here we show reconstructions of the paleohydrology of the East Gobi Desert since the last interglacial using satellite images and digital elevation models (DEM) combined with detailed section analyses. Paleolakes with a total area of 15,500 km2 during Marine Isotope Stage 5 (MIS 5) were identified. This expanded lake system was likely coupled to an 800–1000 km northward expansion of the humid region in East China, associated with much warmer winters. Humid climate across the Gobi Desert during MIS 5 likely resulted in a dustier MIS 4 over East Asia and the North Pacific. A second wet period characterized by an expanded, albeit smaller, lake area is dated to the mid-Holocene. Our results suggest that the East Asian Summer Monsoon (EASM) might have been much weaker during MIS 3.