A large lake plays an important role in mitigating flood disasters in its nearby regions during the flooding period; however, the effect is limited, because most of its storage capacity becomes dead storage prior to the arrival of the flood wave. In the current study, an innovative flood control scheme (IFCS) is applied to Dongting Lake (the second largest freshwater lake in China) to alleviate flood disasters. MIKE 21 FM was used to examine its feasibility to mitigate flood disasters. One of the largest floods in the 20th century, the 1998-type flood, was modelled and the maximum water levels with/without IFCS were compared. The result shows that the effective flood control storage could be at least doubled when compared with the natural condition once IFCS was applied. The peak flood level in the Dongting Lake could be lowered by at least 0.32 m at the Chenglingji station in the same flood passage of Dongting Lake. The case study reveals that, after applying IFCS, the hydraulic gates play a very important role in floodwater regulation and further study should be conducted to find the optimized operation for each gate in the flood control scheme system.