The reservoir flood control operation problem has the characteristics of multiconstraint, high-dimension, nonlinearity, and being difficult to solve. In order to better solve this problem, this paper proposes an improved bald eagle search algorithm (CABES) coupled with ε-constraint method (ε-CABES). In order to test the performance of the CABES algorithm, a typical test function is used to simulate and verify CABES. The results are compared with the bald eagle algorithm and particle swarm optimization algorithm to verify its superiority. In order to further test the rationality and effectiveness of the CABES method, two single reservoirs and a multi-reservoir system are selected for flood control operation, and the ε constraint method and the penalty function method (CF-CABES) are compared, respectively. Results show that peak clipping rates of ε-CABES and CF-CABES are both 60.28% for Shafan Reservoir and 52.03% for Dahuofang Reservoir, respectively. When solving the multi-reservoir joint flood control operation system, only ε-CABES flood control operation is successful, and the peak clipping rate is 51.76%. Therefore, in the single-reservoir flood control operation, the penalty function method and the ε constraint method have similar effects. However, in multi-reservoir operation, the ε constraint method is better than the penalty function method. In summary, the ε-CABES algorithm is more reliable and effective, which provides a new method for solving the joint flood control scheduling problem of large reservoirs.