This study uses the Finite-Volume Community Ocean Model (FVCOM) to simulate the hydrodynamic processes during typhoon “Saola”. The simulation results closely match observed data. Typhoon “Saola” was a major system in the Pacific typhoon season, highlighting the complexity and uncertainty of tropical cyclone dynamics. By analyzing historical sea surface temperature data and the typhoon’s trajectory, the three-dimensional response of sea temperature during typhoon “Saola” was explored. The key findings are as follows: 1. Typhoon passage affects both coastal and deep-sea warming and cooling. Temperature changes are more pronounced near the coast, with the highest warming and cooling occurring within five days after the typhoon. In deep-sea areas, the highest warming occurs within five days, while the lowest cooling occurs within two days. 2. The nearshore water layers respond quickly to the typhoon, while the deep-sea water layers primarily respond in the middle depths, with a delayed effect. 3. In coastal shallow waters, the response is intense, with the maximum temperature increase and decrease occurring near the bottom, reaching 5.26 °C and −5.17 °C, respectively. In deep-sea areas, the response is weaker, with the maximum temperature change occurring near the surface: an increase of 0.49 °C and a decrease of −0.98 °C. The deepest response in coastal waters reaches about 80 m, while in the deep-sea area, it only reaches 50 m due to the thicker mixed layer.