As a key water control project to manage and develop the Yangtze river, the Three Gorges project has profound impact on national economy, society and ecological environment. It not only has played a significant role in defending flood threat of the Yangtze river, but also has created remarkable economic benefits in power generation and river shipping since it was built. To alleviate the adverse impact caused by the operation of the Three Gorges reservoir, ecological operation practice was carried out from 2011 to 2014. In order to promote the ecological operation of the reservoir in the future, the effect of the ecological operation which was carried out during trial run period is scientifically evaluated combining the assessment conclusions of ecological impact of the Three Gorges project in design phase and the monitoring results of ecological operation target in trial run period. Finally some suggestions are put forward for the future ecological operation.