Nuclear power plants applying for license renewal are required to undertake a fatigue assessment of various components, which demands the fast calculation of transient thermal stress of the fatigue-sensitive components such as surge lines. In this study, the strategy of Green’s function database construction for the thermal stratification region was investigated, and the thermal stress calculation was shown to be more accurate by dividing the flow cases and thermal zones. Furthermore, a method to determine the fluid temperature for the thermal zones of the thermal stratification region was studied. In addition to the temperature of the hot leg fluid and the outlet fluid from the pressurizer, seven thermocouples installed on the outside wall in the thermal stratification region were used to determine the fluid temperature of thermal zones with stratification, and the calculation result of the fluid temperature was verified with the temperature Green’s functions.