Aiming at the dual games between impounding time and water storage schemes, flood control target and storage benefit target for the water storage problem of Hongze Lake in post-flood period in high-flow years, a three-dimensional“time-discharge-index” mapping relationship was constructed based on the refined simulation with the hydrological-hydrodynamic model and the idea of combining enumeration water storage strategies and numerical simulation. By coupling of the hydrological-hydrodynamic model with the NSGA-II multi-objective optimal model, optimal regulation rules for discharge under multi-gate combination in post-flood period were extracted. The results show that there is an obvious Pareto competition relationship between flood control risk and water storage benefits in high-flow years, and the two objectives can compensate each other through the replacement relationship. According to the obtained global optimal solution of the water storage strategy for Hongze Lake in post-flood period in a typical high-flow year of 2003, the impoundment should start from September 20th, and the discharge volume is recommended to increase from 1600m³/s to 2213m³/s corresponding to the water level of 13.00m, which can decrease the flood control risk as well as the abandoned water loss.