The Sea of Japan (also termed the East Sea) has a circulation system isolated from the Pacific Ocean and East China Sea. The East Asian winter monsoon drives the circulation system and cools the Tsushima Warm Current (TWC) to form the Japan Sea Intermediate–Proper Water (JSIPW). The intermediate water conveys oxygen to deep-sea floors, which is available for benthic animals. During the Pliocene (3.5–2.8 Ma), Temperate Intermediate Water (TIW) was formed under the weak winter monsoon, and extinct ostracod TIW taxa were found. Little is known about early Pleistocene intermediate water and the extinction mode of benthic ostracods. We studied radiolarians and ostracods from deep-sea sediments between 2.0 and 1.3 Ma (Marine Oxygen Isotope Stage [MIS] 77 to MIS 41) at Integrated Ocean Drilling Program Site U1426, Sea of Japan. The ostracod faunas contained TIW and JSIPW taxa. The radiolarian subtropical-water taxa and the JSIPW ostracods indicate a small influx of the TWC and the JSIPW. The TIW occasionally expanded to the middle bathyal zone. By analogy with the relationship between the modern JSIPW and winter monsoon, weak winter monsoon possibly caused gentle temperature gradients in the water column and the expansion of the TIW. The JSIPW taxa expanded their ranges into the deep sea during interglacial periods.