Abstract: Ecological protection degree for a de-watered river channel is defined based on its minimum ecological flow and suitable ecological flow to reduce the adverse ecological impact of water conservancy projects on the river flows downstream of the reservoirs. A model of optimal ecological operation of reservoirs that maximizes ecological protection degree and power generation is developed and solved using an improved Non-dominated Sorting Genetic Algorithm-II (NSGA-II) algorithm. A case study of the Liujiaping hydropower reservoir demonstrates that the optimization of its ecological operation can protect the ecosystem of the de-watered channel downstream of it, and that the ecological protection degree decreases with the increase of benefit of its power generation. Compared with the scheme of best power generation benefits, our scheme raises ecological protection degree from 0.011 to 0.551 and decreases power generation by 20%. This would generally meet the minimum ecological flow requirements, recovering the flow process as close as possible to the acceptable ecological flow, and thus helpful to practical operation.