The operations of reservoirs produce enormous economic and social benefits but also impact species composition and habitat distribution of the riverine ecosystem. Hence, the realization of conservation and restoration of the ecosystem calls for reservoir reoperation. It is a widespread consensus that providing suitable ecological flow (SEF) for ecosystems is a useful way to cushion adverse effects. In contrast to the conventional methods that take a minimum ecological flow as a constraint, studies have been conducted to establish multi-objective operation models with an ecological objective recently. This paper considers two cascaded reservoirs: the Three Gorges Project (TGP) and the Gezhouba Dam in the middle Yangtze River. By concentrating on urgent ecological problems such as the reproduction of four major species of Chinese carp and the propagation of Chinese sturgeon, a series of monthly SEF was synthesized. Afterward, a long-term multi-objective optimization model that maximizes power generation and minimizes the water volume that violates ecosystem water requirements was developed to study the relationship between the two objectives. The non-dominated sorting genetic algorithm II method was applied to solve the proposed model. The optimized results show that according to the present water control operating regulations, the monthly amount of released water of TGP can be sufficient for ecosystem requirements except in October. The ecological model is better in improving the river ecosystem, but at the expense of power generation loss. Moreover, this method provides a set of operational non-dominated schemes between the target objectives for decision-makers to select and could be useful for water resource management of reservoirs.