The construction of inter-basin water diversion projects is one of the important means to solve the uneven distribution of water resources in the world. This article introduces inter-basin water diversion projects at home and abroad and summarizes the water ecological and environmental impacts caused by inter-basin water diversion projects, including the water environmental impacts on conventional water quality indicators, dissolved organic matter, water eutrophication, and water pollutants, as well as the water ecological impacts on biological invasion and biodiversity. It sorts out the research methods of water ecological structure, providing a theoretical basis for further exploration from the perspective of ecological structure mechanism. Finally, it puts forward the research trends and development suggestions of water ecology in inter-basin water diversion projects.