Abstract: Scientific determination of wind wave run-up is a critical step in rationally defining the inundation scope of reservoir areas and ensuring safety. This study systematically investigated the theoretical basis for wind wave run-up calculation as stipulated in the "Design Code for Land Acquisition and Resettlement Planning of Water Resources and Hydropower Projects (SL290-2009)", thoroughly analyzing the determination methods and intrinsic mechanisms of key factors such as vertical wind speed over reservoir surfaces, fetch length, slope gradient, and roughness coefficient. Then the Three Gorges Reservoir on the Yangtze River and the Danjiangkou Reservoir, the water source for the South-to-North Water Diversion Middle Route, were selected as case studies. The wind-driven wave run-up calculations of the two reservoirs were conducted by integrating long-term operational data and detailed topographic information. Furthermore a global sensitivity analysis based on the Sobol sequence was introduced to quantify the influence weights of various factors. The results indicated that under the condition of multi-year average wind speed, the maximum wind wave climbing height of the typical section of the Three Gorges Reservoir is 0.06 m, while in the Danjiangkou Reservoir, it can reach 0.33m. However, when adopting the 10% frequency design wind speed, the maximum wind-driven wave run-up at typical sections of the Three Gorges Reservoir increases to 0.53m, and in the Danjiangkou Reservoir, it can reach 1.76m, which highlights the significant influence of the wind speed value standard on the calculation results. Additionally. Under the same design wind speed criteria, affected by differences in reservoir morphology, the wind wave run-up of the Danjiangkou Reservoir is considerably higher than that of the Three Gorges Reservoir. Moreover, due to the wider reservoir surface, the wind wave run-up in the Danjiang section of the Danjiangkou Reservoir is generally higher than that in the Hanjiang section. Meanwhile, he sensitivity analysis reveals that slope gradient and wind speed are the two most influential parameters affecting wind-driven wave run-up, with a strong interactive effect between them.