This paper uses the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) model to analyze the impact of typhoon “Hongxia” on the velocity and position movement of the Kuroshio axis, the impact of typhoons on the Kuroshio intrusion into South China Sea (SCS), the corresponding water, heat, and salt fluxes, and the impact of Kuroshio water in the northeastern SCS. When typhoon “Hongxia” passed, the Kuroshio intrusion into the SCS was the most significant at 21°N latitude. In the vertical direction, the Kuroshio intrusion was strongest in the subsurface layer, leading to the most significant changes in temperature and salinity in the northeastern part of the SCS in the subsurface layer. Under the influence of the southeastern monsoon in summer, a large amount of low-salinity water accumulates at the surface of the northeastern part of the SCS, and Kuroshio intrusive water remains in the bottom and middle portions of the subsurface layer. The westward deviation of the Kuroshio axis caused by the typhoon displays a certain lag compared with the hot and salty water intrusion into the SCS approximately 7 d later. The impact of the typhoon on the Kuroshio intrusion into the SCS lasts for 20 d. The typhoon caused increases in the water, heat, and salt fluxes associated with the Kuroshio intrusion into the SCS, and the contribution of the typhoon to these fluxes was as high as 40%. Under typhoon conditions, the maximum Kuroshio intrusion flux reached more than twice that before the typhoon.