Coastal areas have become the primary location for nuclear power plant sites due to the convenience of seawater cooling. In China, the diffusion range of thermal discharge water has always been a hot research topic as the basis for sea use areas. The main physical process of heat loss in the numerical simulation of thermal discharge from power plants is heat exchange between the water surface and air. Currently, the methods for calculating this heat loss include the heat flux method and the water surface heat exchange coefficient method. Taking a power plant in Zhejiang as the research object, the MIKE 3 temperature–salinity module (heat flux method) and MIKE ECO Model (water surface heat exchange coefficient method) were used for modeling, and the diffusion of thermal discharge water under different modules was compared and analyzed. The results show that the calculated area of the water temperature rise envelope between the two modules differed significantly under the same conditions. The surface 4 °C temperature rise area, as calculated using ECO Model, was 45.8% smaller than that of the temperature–salinity module. The MIKE 3 temperature–salinity module can simulate the heat accumulation of water under thermal buoyancy, producing a significant thermal stratification phenomenon; the ECO module does not accurately represent the heat exchange process between the water surface and the air, and it does not adequately capture the significant vertical stratification that occurs in real-world scenarios. On this basis, this study not only lays a foundation for further exploring the impact of thermal discharge water from this powerhouse on the structure of surrounding marine biological communities and dissolved oxygen content in water bodies but also provides scientific evidence for the selection of modules when simulating thermal discharge water with the MIKE model.