The East Asian winter monsoon (EAWM) has a profound effect on the winter climate in East Asia. The modern EAWM variability is tightly linked to the high-latitude Northern Hemisphere climate change through the Siberian High and can also be regulated by the low-latitude El Niño-Southern Oscillation through oceanic or atmospheric teleconnections. However, the Quaternary EAWM evolution has long been only attributed to the high-latitude climate change, resulting in the uncertainty in interpreting the out-of-phased EAWM variation recording in the East Asian continent and marginal seas. Here we presented a sediment record at Integrated Ocean Drilling Program Site U1427 in the southern Japan Sea to reconstruct the EAWM evolution since the last glacial maximum. By combining our record with previous reconstructions and simulations, we found the synchronous relationship between winter monsoon in northern and southern regions of East Asia from ∼24 to 8 ka, but anti-correlated relationship since ∼8 ka. We proposed the winter insolation and Atlantic meridional overturning circulation were the main drivers from last glacial to early Holocene, and then ENSO became a dominant factor in controlling the regional heterogeneity of EAWM evolution in the middle and late Holocene. This research explains much of the controversy in the Quaternary EAWM records and highlights the low-high latitude interaction in East Asian winter climate change.