Reservoir flood control operation (RFCO) is a complex problem that involves various constraints and purposes, which include the safety of the dam, watershed flood control and navigation. These objectives often conflict with each other. Thus, traditional methods have difficulty in solving the multi-objective problem efficiently. In this paper, a multi-objective self-adaptive electromagnetism-like mechanism (MOSEM) algorithm is introduced in the local searching operation of the proposed method. To enhance the optimization ability of EM, a self-adaptive parameter is applied in the local search operation of MOSEM for adjusting the values of parameters dynamically. Moreover, MOSEM is tested by several benchmark test problems and compared with some well-known multi-objective evolutionary algorithms. A case study is also used for solving RFCO problems of the Three Georges Reservoir by using the multi-objective cultured differential evolution (MOCDE), non-dominated sorting genetic algorithm-II (NSGA-II) and proposed MOSEM methods. The study results reveal that MOSEM can provide alternative Pareto-optimal solutions (POS) with better convergence properties and diversification.