The South China Sea is one of the major marginal seas in the world and is located in the tropical region, making it an important area for tropical climate and monsoon systems. The sedimentary environment and sediment supply in the South China Sea are stable, making it an ideal area for studying paleoclimate change. The core MD102364 (119.33°E, 21.54°N, water depth 2890 m) is approximately 23 meters long and was taken from the northern slope of the South China Sea near Taiwan Island. The reconstructed age model shows that the core covers a time span of approximately 50,000 years. This core mainly receives sediments from Taiwan, and because the Kuroshio Branch, influenced by the hydrological conditions of the equatorial Pacific, intermittently invades the South China Sea and flows through the core area, the sediment records from this region can appropriately reflect long-term changes in the Kuroshio Branch. This study analyzes the fossil shells of the surface-dwelling planktonic foraminifera Globigerinoides ruber, the thermocline-dwelling Neogloboquadrina dutertrei, and the subsurface-dwelling Pulleniatina obliquiloculata. By measuring their stable carbon and oxygen isotopes and Mg/Ca ratios, we reconstruct temperature and seawater oxygen-isotope records at different water depths over the past 50,000 years. Differences among the three species are used to investigate changes in the vertical temperature structure and water-column stratification of the northern South China Sea. Comparison with other reconstructed records from the surrounding South China Sea will help clarify the responses of regional upper-ocean conditions to changes in the Kuroshio Current, East Asian monsoon, and glacial–interglacial climate variability.