Abstract: The Gezhouba Dam (GD) and the Three Gorges Dam (TGR) are the world’s largest cascade hydropower stations, which have a comprehensive efficiency on flood control, power generation, navigation and irrigation in the middle and lower reaches of the Yangtze River. However, before the construction of the GD and TGD, it had undergone a long-term debate on how to mitigate their influence on the ecological environment and aquatic organisms of the Yangtze River. Throughout this process, the Institute of Hydrobiology, Chinese Academy of Sciences (IHB) made a great contribution to evaluating the impact of GD and TGD on the fish resource of the Yangtze River and mitigation measures. In the discussion of conservation priority, the IHB pointed out the Chinese sturgeon was the most critically endangered species. To save this species, the IHB demonstrated Chinese sturgeon could reproduce naturally below the GD and the artificial propagation and spawning ground protection were the main conservation measures, which could be used as the substitute for the unnecessary measures of fish passages. After the construction of GD, the IHB further predicted the TGD would have adverse effects on the fish resources of the Yangtze River and suggested establishing the Chishui National Nature Reserve, which could give shelter to the rare and endemic fishes in the upstream Yangtze River. With the impoundment of the Three Gorges Reservoir (TGR), the IHB first proposed to create artificial floods to induce the spawning of four major Chinese carp species. This is the so-called “ecological schedule”. Up to time now, most of the mitigation measures proposed by the IHB had been proved scientific and effective. For the long-term efforts to fish protection, the IHB has played a positive role in the ecological conservation of the Yangtze River and sustainable development of fishery resources.