A large number of basins in China are facing problems such as the degradation of ecosystems and decline of biological resources. This paper is devoted to illustrating the influence of large water conservancy and hydropower projects on major aquatic species in rivers, and demonstrating key technologies for control and regulation, which could help to provide technical support for aquatic ecological civilization construction and ecological conservation. With focuses placed on large rivers in China, such as the Yangtze River, this paper provides a review of the current status and trends of four major Chinese carp and the Chinese sturgeon influenced by large water conservancy and hydropower projects. Based on analysis of the stress effects of these projects on the habitats of major aquatic species, the regulation potential for natural reproduction of the aquatic species as well as possible approaches are discussed. Using a large water conservancy and hydropower project as a case study, the key technologies for optimal regulation of the project in order to increase the natural reproduction of major aquatic species and the applicability of these technologies are discussed.