Aeolian dust input exerts significant influence on oceanic biogeochemical cycles and further potentially controls atmospheric CO2 concentrations. However, the possible link between long-term aeolian dust supply and primary productivity in the western North Pacific remains poorly understood. Here, we present a comprehensive study of major and trace elements and total organic carbon (TOC) concentrations of sediments from Integrated Ocean Drilling Program (IODP) Site U1430 in the southern Japan Sea, in order to reconstruct oceanic palaeoproductivity evolution and test its possible link to Asian dust input since 4 Ma. Palaeoproductivity proxies indicate remarkable increases in productivity at ∼3–2 Ma followed by high-frequency oscillations in productivity since 1.2 Ma. We suggest that higher dust-derived iron supply from Central Asia at 3–2 Ma, which was likely driven by the growth of the Northern Hemisphere ice sheets, could account for enhanced primary productivity and export production in the Japan Sea. Such increased oceanic palaeoproductivity could enhance organic carbon burial, which might contribute to the decrease in atmospheric CO2 concentrations, and provide a positive feedback to the global cooling. However, the Tsushima Warm Current (TSWC) intrusion via the southern Tsushima Strait, which was controlled by glacioeustatic sea level changes, has been the principal cause of the rapid changes in primary productivity and benthic redox condition since 1.2 Ma, regardless of continuously increased Asian dust input.