The research of joint optimization operation of complex flood control systems is still in the process of development. This paper introduces a decomposition–coordination model for solving the multi-objective optimization problem for real-time flood control operation in reservoir group and flood storage basin. The multi-objective programming is established for maximum safety of the reservoir group and minimum losses of flood storage basin, according to the real-time flood control requirements. Then, a third-order hierarchical optimization decomposition–coordination model is proposed for solving the multi-objective programming problem, based on the decomposition–coordination principle of large scale system theory. It takes advantage of an objective coordination method and model coordination method to accomplish global optimization and combines progressive optimality algorithm to solve the subsystem local optimization. Finally, the model is applied for simulating the storm flood in July 2007 in the middle reaches of the Huaihe River Basin in China. Results show that the proposed decomposition–coordination model can efficiently calculate the reservoir group optima release strategy and flood storage basin diversion process, and meet the safety discharge at the downstream control section.