A mesoscale model coupling the Weather Research and Forecasting model and the three‐dimensional Price‐Weller‐Pinkel ocean model is used to investigate the dynamical ocean response to Megi (2010). It is found that Megi induces sea surface temperature (SST) cooling very differently in the Philippine Sea (PS) and the South China Sea (SCS). The results are compared to the in situ measurements from the Impact of Typhoons on the Ocean in the Pacific (ITOP) 2010 field experiment, satellite observations, and ocean analysis field from Eastern Asian Seas Ocean Nowcast/Forecast System of the U.S. Naval Research Laboratory. The uncoupled and coupled experiments simulate relatively accurately the track and intensity of Megi over PS; however, the simulated intensity of Megi over SCS varies significantly among the experiments. Only the experiment coupled with three‐dimensional ocean processes, which generates rational SST cooling, reasonably simulates the storm intensity in SCS. Our results suggest that storm translation speed and upper ocean thermal structure are two main factors responsible for Megi's distinct different impact over PS and over SCS. In addition, it is shown that coupling with one‐dimensional ocean process (i.e., only vertical mixing process) is not enough to provide sufficient ocean response, especially under slow translation speed (~2–3 m s−1), during which vertical advection (or upwelling) is significant. Therefore, coupling with three‐dimensional ocean processes is necessary and crucial for tropical cyclone forecasting. Finally, the simulation results show that the stable boundary layer forms on top of the Megi‐induced cold SST area and increases the inflow angle of the surface wind.