The invention discloses a method and a system for optimal scheduling on joint flood control for cascade reservoir groups. The method includes the steps of firstly, determining flood type according to real-time reservoir level and the process of forecasting runoff in case of flood; secondly, deciding a primary protection object according to the flood type and downstream control-point flood control standards; thirdly, automatically selecting flood control optimization objectives and corresponding optimization scheduling models in a system model base; and fourthly, solving and optimizing the optimization scheduling model by modified genetic algorithm. The method and the system dynamically judge the level of flood and finish hierarchical scheduling based on the level of flood. In addition, projection of downstream protection objects, dam safety and flood recycling are achieved by selecting proper optimization scheduling objectives according to comprehensive information of the reservoirs, such as regulation performance, scheduling period and reliability in forecast flood during hierarchical scheduling, efficiency in decisions for the reservoir groups is improved, and mass data statistics show that the decision efficiency is improved by about 30% by the method and the system.