Traditional reservoir operation ignores ecological demands of rivers. This would probably lead to degradation of river ecosystem. In order to alleviate the influence of reservoirs on river ecosystem, multi-objective reservoir ecological operation was proposed from perspective of maintaining the river ecosystem health. Multi-objective mathematical model of multi-reservoir ecological operation was established. A multi-objective particle swarm optimization (MOPSO) algorithm was introduced to generate a set of Pareto-optimal solutions. In addition, to facilitate easy implementation for the reservoir operator, a simple but effective decision-making method was presented to choose the desired alternative from a set of Pareto-optimal solutions. Finally, the proposed approach was applied to the ecological operation of the reservoirs at the main stream of Xiuhe river in Poyang Lake basin in China. The results show that the proposed approach is able to offer many alternative policies for the water resources managers, and it is a viable alternative to solve multi-objective water resources and hydrology problems.