Evidence from ecological studies has suggested that alteration of river flows downstream of reservoirs can threaten native aquatic ecosystems. The Three Gorges Reservoir has been controversial since its design and construction stage, and the ecological damage downstream is an important concern. However, protecting long-term health of the river ecosystem has a low priority in reservoir operation compared to other human demands, and is traditionally treated as a constraint of minimum water release. A multi-objective reservoir optimization model incorporating ecological adaption is proposed. Range of variability approach is first used to quantify the hydrological alteration. A satisfying ecological flow scenario is then worked out if it is necessary to take ecological issues into consideration. With the aim of eco-compensation, the reservoir release should be as close to satisfying ecological flow as possible, which is set to be the objective for ecological adaption. Together with other objectives, such as flood control and power generation, a multi-objective optimization model is established, which is optimized by NSGA-II algorithm. Results not only provide the operational references in both wet and dry years, but also illustrate the negative impacts on the river ecosystem by reservoirs can be alleviated with low economic cost. Quantitative relationships among different objectives can also be used for trading markets.