The North Pacific Subtropical Gyre (NPSG) has two important functions, i.e., one in ocean heat transfer and another as a driving force for circulation of the surface and intermediate waters on the basin scale. In the present study, we describe records of the vertical thermal structures and distributions of water masses in the upper ocean of the subtropical northwest (NW) Pacific for the past 190 kyr, using two sediment cores collected from the Kuroshio Current area in the East China Sea and the NPSG area. During the two glacial periods, the Kuroshio Current was weakened owing to changes in ocean-atmosphere circulation and eustasy. The differences in the Mg/Ca-derived temperatures between surface and thermocline waters show the changes of depth and temperature (warming) of thermocline during glacial periods. Conversely, the planktonic foraminiferal assemblages demonstrate that the indicator of the intermediate water from the central area of the NPSG increased synchronously with thermocline warming during marine isotope stage (MIS) 6. These results suggest that warm intermediate water strongly affected the changes in the water-column structure of the subtropical NW Pacific during MIS 6. However, during MIS 2, cold water had precedence over intermediate water probably owing to the southward shift of the subtropical front associated with the reduced transport of the Kuroshio Current. Thus, the NPSG has evolved differently during the two glacial periods (MIS 2 and MIS 6) through interactions between the Kuroshio Current, surface water, and intermediate water.