Based on the measured topography data of Dongting Lake in 2003 and 2011, a previous calibrated 2D hydrodynamic model was adopted to simulate the impact of lake topographic change on the flood process of Dongting Lake using the 2003 flood as an example. The results show that over 40% topography of the lake subsided more than 0.10 m, especially the Xiangjiang spillway, the topography of its talweg subsided by 5.72 m. According to the simulation of the 2003 flood process, when the flood process was dominated by the Four Rivers, the flood peak water level decreased by more than 0.40 and 0.20 m in the South and West Dongting Lake under the topographic condition of 2011 compared with that of 2003; but for the East Dongting Lake, the water level only decreased significantly in the southern area with large topographic changes. The water surface gradient decreased in the Doumizui-Chenglingji section, but increased in the spillway of the South Dongting Lake. For the flood process dominated by the inflow of the Yangtze River, the flood peak water level in Dongting Lake decreased by 0.15 m, and the water surface gradient changed little in the Doumizui-Chenglingji section and the South Dongting Lake, due to the jacking effect of the Yangtze River. Therefore, the topographic change in Dongting Lake from 2003 to 2011 has a great impact on the flood dominated by the inflow of the Four Rivers, which can effectively alleviate the flood control pressure in Dongting Lake because the entrenchment of the lake basin increased the storage capacity of the lake; however, it has little impact on the flood dominated by the inflow of the Yangtze River. The research results can provide a reference for the implementation of flood control measures such as dredging and capacity expansion in Dongting Lake.