Yellow Sea current conditions during the late Marine Isotope Stage 3 (late MIS3, 40–30 ka B.P.) highstand remain unknown. Here, environmental magnetism, geochemistry, particle size, and scanning electron microscope methods are employed to analyze core YS01A with a basal age of 40 kyr from the South Yellow Sea mud deposits. Greigite formed in marine sedimentary layers with thickness >7 m during early diagenesis. Greigite formation is related to the redox state and total organic content (TOC) availability, which are controlled, respectively, by the Yellow Sea Cold Water Mass (YSCWM) and the Yellow Sea Warm Current (YSWC). In MIS1 (7–0 ka B.P.), a strong YSWC brought greater TOC, and a strong YSCWM (thickness of 48 m) resulted in a strongly reducing low-oxygen environment. This led to massive magnetite dissolution and pyrite preservation. In late MIS3 (37–31 ka B.P.), the weak Kuroshio Current and East Asian Winter Monsoon (EAWM) resulted in a low-intensity YSWC that provided less TOC. A weak YSCWM (thickness of 35 m), caused by shallow water depths and a weak EAWM, contributed to a less reducing sedimentary environment. Thus, pyritization was interrupted and greigite was preserved. Greigite content can, thus, be used to trace the development of Yellow Sea currents. During a period of slow sea level rise at 41–37 ka B.P., minor greigite formed with most magnetite being preserved, which indicates that the environment started to become reducing. This can be interpreted as due to initial formation of a thin and weak YSCWM. During the 37–31 ka B.P. highstand, the greigite content increased, which suggests more reducing conditions related to establishment of a thicker and intensified YSCWM. In addition, the greigite content decreased progressively, which may have resulted from YSWC weakening. Our results suggest that greigite can be used as a simple tool to reflect current evolution in the Yellow Sea, which can give a better understanding of continental shelf environment change.