Deepwater circulation plays a central role in global climate. Compared with the Atlantic, the Pacific deepwater circulation’s history remains unclear. The Luzon overflow, a branch of the North Pacific deep water, determines the ventilation rate of the South China Sea (SCS) basin. Sedimentary magnetic properties in the SCS reflect millennial-scale fluctuations in deep current intensity and orientation. The data suggest a slightly stronger current at the Last Glacial Maximum compared to the Holocene. But, the most striking increase in deep current occurred during Heinrich stadial 1 (H1) and to a lesser extent during the Younger Dryas (YD). Results of a transient deglacial experiment suggest that the northeastern current strengthening at the entrance of the SCS during H1 and the YD, times of weak North Atlantic Deep Water formation, could be linked to enhanced formation of North Pacific Deep Water.