Under the new inflow and outflow patterns of Hongze Lake, a two-dimensional hydrodynamic model was established to investigate the impact of elevated water control levels during flood season on water levels and operational scheduling of the lake. The variation characteristics of the water level at Jiangba in the lake area under the conditions of elevated water control levels and the lakeside projects were analyzed. According to the dispatching rules for flood detention areas in Hongze Lake, suggested values for the water control levels during flood season for different combinations of water inflows and lakeside projects were given. The results show that the second stage of the project on the sea-entering channel can significantly reduce the peak water level at Jiangba when the current water control level of Hongze Lake is 12.5 m. The Fengtieying River Diversion Project has almost no impact on the water level at Jiangba under the synergistic effect of the project on the sea-entering channel. For a flood event with the same magnitude in 2007, the water control level within 14.0 m does not increase the flood risk in the detention area around the lake. Therefore, the water control levels of Hongze Lake during flood season can be raised by 1.0-1.5 m. Under the condition of the once-in-a-century flood event, the peak water level at Jiangba will not change when the water control level remains within 14.0 m. However, the elevated water control level can cause the detention area to open ahead of time, and the water control level can be raised by 0.5-1.0 m without increasing the flood risk in the detention area.