Analysis both based on the wind stress and ocean assimilation dataset shows that the interannual variability of the Indonesian Throughflow and the South China Sea (Luzon Strait) Throughflow is out of phase. Wind anomaly forcing in the equatorial Pacific plays an important role in setting up this phase relation. During El Ni o events, the westerly wind bursts intensify the Northern Equator Current and induce a northward shift of its bifurcation point. As a result, the partition of volume transport between the Kuroshio and the Mindanao Current is changed, with the Kuroshio transport decreased and the Mindanao Current increased. The undershooting/overshooting phenomena occur at the Luzon Strait and the Sulawesi-Mindanao passage, caused by variability of these two currents. Water transport from the Pacific to the South China Sea increases with the Kuroshio transport decreased, and transport from the Pacific to the Indian Ocean decreases with the Mindanao Current transport increased. The situation is reversed during La Ni a. Therefore, the ocean dynamic meaning is profound to study the interannual variability relationship between the Indonesian Throughflow and the Luzon Strait Throughflow. Analysis both based on the wind stress and ocean assimilation dataset that that interannual variability of the Indonesian Throughflow and the South China Sea (Luzon Strait) Throughflow is out of phase. Wind anomaly forcing in the equatorial Pacific plays an important role in setting up this phase relation. During El Ni o events, the westerly wind bursts intensify the Northern Equator Current and induce a northward shift of its bifurcation point. As a result, the partition of volume transport between the Kuroshio and the Mindanao Current is changed, with the Kuroshio transport decreased and the Mindanao Current increased. The undershooting / overshooting phenomena occur at the Luzon Strait and the Sulawesi-Mindanao passage, caused by variability of these two currents. Water transport from the Pacific to the South China Sea increases with the Kuroshio transport decreased, and transport from the Pacific to the Indian Ocean decreases with the the Mindanao Current transport increased. The si Therefore, the ocean dynamic meaning is profound to study the interannual variability relationship between the Indonesian Throughflow and the Luzon Strait Throughflow.