Deep-water circulation in the South China Sea is closely linked to deep hydrography of the North Pacific via water exchange at the Luzon Strait. In this study, temporal changes of the paleocurrent intensity in the South China Sea are established using the detrital sortable silt proxy to reconstruct the evolution of deep hydrography of the subarctic Pacific since the last deglaciation. The results show that deep (>1500 m) currents in the South China Sea were relatively vigorous during the last glacial period, and relatively weak during the Holocene. A gradual decrease of current speed during the last deglaciation was observed at both ~1650 m and ~ 2000 m water depths. Furthermore, the current-intensity decline started earlier in relatively shallow portion (~1650 m) than in deep portion (~2000 m). This disparity is interpreted to be associated with the gradual deepening of the glacial North Pacific Intermediate Water, which reduced the pressure gradients between the Pacific and the South China Sea at the depth levels it affected. Such processes also greatly altered the stratification in the South China Sea: a strong stratification existed prior to the Heinrich Stadial 1, but it vanished owing to the enhanced vertical mixing brought by downward penetration of the glacial North Pacific Intermediate Water. Our study provides new insights into the evolution of deep hydrography in the subarctic Pacific, and the processes how such changes affect the subtropical Pacific under glacial boundary condition.