In this study, a methodology was devised to overcome that difficulty for thermal stratification modeling using EFDC. For the increase of reproductability for thermal stratification analysis, the effect of parameter such as distribution of solar radiation, depth of active bed temperature layer, heat transfer coefficients were analyzed. The simulation period was from June to December in 2005 and statistical index is used to analyze the model results. The results showed that distribution of solar radiation is zero and depth of active bed temperature layer is 10 m are suitable for simulation of thermal stratification in Yongdam Dam reservoir. This study results can be used for guideline to analyze the thermal stratification of large dam reservoir in Korea.