Paleoceanographic conditions in the Japan Sea changed drastically during the Late Quaternary in association with orbital and suborbital cycles and glacio-eustatic sea level changes. However, few studies have examined long-term sediment records older than 160 ka because of the lack of long and continuous cores and the difficulty in constructing high-resolution age models. In this study, we first constructed an orbital-scale stratigraphy of the sediments covering the last 640 kyr by comparing the SPECMAP ∂ 18O curve and the ∂ 18O curve of planktonic foraminifera ( ∂ 18O pf) in the Japan Sea together with the combination zones of dominant planktonic foraminifera species. Then, we reconstructed temporal variations in biogenic silica (BioSil) and biogenic carbonate (BioCarb) contents calculated from high-resolution major element analysis data determined by an XRF microscanner. In order to evaluate the deep-water oxygenation conditions, we also defined excess S as the difference between the content of S in the sediments and that for normal marine sediments calculated from the organic carbon content (C org) estimated from lightness ( L ⁎) by assuming a total sulfur content (S total)/C org ratio of 0.36, and examined its variability. BioSil shows orbital-scale variation and is generally low except during interglacial maxima when global sea level was high enough to allow a strong influx of the Tsushima Warm Current. BioCarb shows orbital- and suborbital-scale variations and tends to be higher in dark layers deposited during glacial stages, whereas the relationship is reversed during interglacial stages. The low BioCarb in dark layers deposited during interglacial stages is probably due to dissolution of biogenic carbonate caused by the increase in surface productivity as a result of the strong influx of nutrient rich East China Sea Coastal Water and consequent increase in surface productivity and decomposition rate of organic matter in the intermediate water. Excess S tends to be higher in thicker dark layers deposited during glacial maxima when the sea level dropped below − 90 m compared to adjacent light layers, suggesting development of euxinic deep-water conditions during these periods. The results demonstrated the presence of orbital- and suborbital-scale variations in BioSil and BioCarb and their association with dark and light layers in the Japan Sea that reflect variations in the nature and strength of inflow through the Tsushima Strait controlled by both climatic and sea level changes, whereas higher excess S reflects the development of euxinic deep-water condition during glacial maxima in association with glacio-eustatic sea level drops below − 90 m during the last 640 kyr.