Based on the geographical and topographical characteristics of Hongze Lake, the MIKE platform was introduced to build a hydrological-hydrodynamic model for the incorporated system of the lake and its flood detention basin to realize an elaborate simulation of flow movement and water exchange and control between lakes and lands. Then, we developed a water storage strategy sample library composed of different impounding times and water storage schemes in the post-flood period, and carried out large-scale numerical simulations under various inflow scenarios, including high-flow, medium-flow, and low-flow scenarios. Finally, water storage strategies for different typical years were selected and evaluated. The results show that when facing a high-flow period, the impounding time should be set later between September 10th and September 20th, and a scheme of discharge before storage with higher discharge efficiency is recommended, in which a complete flood process should be avoided as far as possible; when facing a medium-flow period, the impounding time should be set earlier between September 10th and September 20th, starting in the flood recession stage, and a scheme of discharge before storage with relatively low discharge efficiency is recommended; when facing a low-flow period, the impounding time should be set between August 31st and September 10th, and a scheme of storage before discharge is recommended, in which the selection of discharge scale should be combined with flood forecasts, and the flood should be intercepted and stored in the rising or middle stage.