The inconsistency between water consumption and the annual rainfall distribution makes it important to make full use of the flood water resource. The adjustment of the flood limited water level (FLWL) is an effective way to improve the flood water utilization, where the staged control of the FLWL plays an important role. Flood season segmentation is the basis for determining the FLWL and tapping the utilization potential of flood resources. The circular distribution method is used to segment, and the relative frequency method is used to verify. Maintaining the balance between benefit and flood control safety is the key work for the FLWL decision. The performances of water supply and hydropower generation are selected to be benefit index, and the extreme risk rate is risk index. Based on the game theory, the multi-objective cooperative decision-making model is established. Nash negotiation solution of staged FLWL is obtained by Nash negotiation theorem. The optimal scheme is determined according to the fuzzy pattern recognition theory. A reservoir is taken as an example, firstly, considering that the risk and benefit are equally valued, the FLWL of the optimal scheme in the pre-flood season is 129.0m, and the post-flood season is 128.5m. By adjusting the preference value for risk and benefit, the optimal FLWL scheme under different preferences for risk and benefit in each stage is determined.