To provide substantial information of extreme water level fluctuations (EWLF) on thermal stratification at Lake Qiandao, the DYRESM model was used to simulate water levels at different scenarios with lack of observed water temperature. This study set up two scenarios including one with EWLF (scenario 1) and the other one with normal hydrological condition (scenario 2) to compare their vertical structure of water temperatures. Based on Lake Analyzer, the depths of top and bottom of thermocline, thermocline thickness and Schmidt stability were calculated for both two scenarios. The results show that the water was mixed during November 20th 2013 to March 23th 2014 in scenario 1 and was mixed during December 5th 2013 to March 16th 2014 in scenario 2. The vertical water temperature structure followed a pattern of “mixed layer-thermocline-hypolimnion (30-40 m)-thermocline-hypolimnion” from top to bottom in scenario 1 and it followed a pattern of “mixed layer-thermocline-hypolimnion” from top to bottom in scenario 2 with the same meteorological conditions. The average water level in scenario1 was less than that in scenario 2 by 2.24 m. Schmidt stability in scenario 1 was also less than that in scenario 2 by 119.19 J/m2, showing that the extreme low water level will significantly reduce the water stability.