As more and more water projects are built on rivers, the flood control operation becomes more complex. Studies on the optimal flood control operation are very important to safeguard human life and property. This study focused on optimizing the operation of a complex flood control system composed of cascade reservoirs, navigation-power junctions, flood storage areas, and flood control points. An optimal model was established to jointly maximize flood peak reduction rates of downstream flood control points. A hybrid algorithm named the Dynamic Programming-Progressive Optimality Algorithm (DP-POA) was used to solve this model, and the middle and lower reaches of the Ganjiang River were selected as a case study. The results show that flood reduction at three downstream flood control points ranged from 1080 to 5359 m³/s for designed floods with different return periods, which increased by about 333~1498 m³/s in comparison with the conventional operation. Considering that the maximum water level of reservoirs using DP-POA and the conventional operation is the same, this indicated that DP-POA can make full use of the reservoirs’ flood control storage to reduce downstream flood peaks. In addition, the flood diversion volume of the flood storage area using DP-POA ranged from 0.33 × 10⁸ to 1.79 × 10⁸ m³ for designed floods with 200-year, 300-year, and 500-year return periods, which is smaller than that using the conventional operation.