The response of the South China Sea (SCS) to Typhoon Chanchu (2006) was examined using the MM5 and POM model. In the POM model, sea surface boundary conditions were forced by the simulation wind field from MM5, the velocity forcing was introduced in the east boundary and the computational schemes of heat fluxes at the surface were introduced. Comparison with the observation data shows that the simulated results are reliable. In the response process of the SCS to Typhoon Chanchu, the influence of the heat fluxes on thermal structure of the SCS was regionally different. Strong wind forcing would lead to upwelling phenomenon in the lateral boundary of deep water basin. Furthermore, the Ekman pumping theory was used to discuss subsurface upwelling and downwelling phenomenon in typhoon forced stage.