We reconstructed the paleoceanographic evolution of the Japan Sea over the Pleistocene using benthic foraminiferal and organic geochemical records from sediment cores recovered at IODP Site U1426, which was drilled at a water depth of 900 m on the Oki Ridge in the southern Japan Sea. The dominant benthic foraminiferal biofacies and the assemblage composition, total organic and inorganic carbon, coarse fraction percentages indicate a notable reduction in primary productivity between 2150 and 1700 ka, due to the restricted supply of nutrients from the northern Pacific Ocean through the northern connecting strait. The inflow of the Tsushima Warm Current via the southern strait began after 1700 ka and marked a major change in the productivity regime of the Japan Sea, as shown by the increased abundance of calcareous foraminifera and enhanced CaCO3 (%). A marked shift in productivity occurred during the Middle Pleistocene Transition, as indicated by the dominance of low-oxygen tolerant species, and a higher influx of total organic carbon (%). The onset of more extreme glaciation at ~490–470 ka coincident with the Mid-Brunhes Event was linked to marked changes in foraminiferal assemblage composition, reflecting major changes in sea-level, oxygen availability at the seafloor, and carbonate compensation depth during intense glacial-interglacial cycles. Productivity changes were also modulated by 23 kyr variability, related to precessional insolation forcing at low latitudes, and superimposed on the 41 and 100 kyr variability, linked to high-latitude climate fluctuations.