Abstract Millennial-scale climate change is thought to be synchronous throughout the Northern Hemisphere and has been demonstrated to be strongly modulated by longer-term glacial–interglacial and orbital-scale processes. However, processes that modulate the magnitude of millennial-scale variability (MMV) at the glacial–interglacial time scale remain unclear. We present multiproxy evidence showing out-of-phase relationships between the MMV of East Asian and North Atlantic climate proxies at the eccentricity band. During most late Pleistocene glacial intervals, the MMV in North Atlantic SST and East Asian monsoon (EAM) proxies shows a gradual weakening trend from glacial inceptions into glacial maxima, inversely proportional to that of the North Atlantic ice-rafted detritus record. The inverse glacial age trends apply to both summer and winter monsoon proxies across the loess, speleothem, and marine archives, indicating fundamental linkages between MMV records of the North Atlantic and East Asia. We infer that intensified glacial age iceberg discharge is accompanied by weakened Atlantic meridional overturning circulation via changes in freshwater input and water column stability, leading to a reduction in North Atlantic SST and wind anomalies, subsequently propagating dampened millennial-scale variability into the midlatitude East Asian monsoon region via the westerlies. Our results indicate that the impact of North Atlantic iceberg discharge and the associated variability in water column stability at the millennial scale is a primary influence on hydroclimate instability in East Asia.