The water conservancy is the foundation support of social and economic development, the water conservancy engineering construction and the coordination relationship between ecology, economy and society affect regional economic, social and ecological development, the water conservancy engineering construction and operation are related to the development and change of our country’s ecological environment, we need to follow the basic policy of human and nature in harmony and coexistence, and vigorously strengthen the ecological civilization construction. In this paper, the application of eco-economic evaluation in small and medium-sized river water conservancy projects is discussed, and the eco-economic evaluation of various water conservancy projects is sorted out based on ecology, economics and ecological economics theories combined with relevant research results, the relationship between water conservancy project construction and ecological economy is studied.Based on the existing cognition of ecological and economic evaluation of water conservancy project, this paper sorted out the research and application status of ecological and economic evaluation of water conservancy project.The relevant theories and evaluation methods of ecological economy evaluation of hydraulic engineering are summarized, as well as the existing problems in ecological economy evaluation of hydraulic engineering. From the evaluation index system and evaluation method, this paper puts forward the research prospect of ecological economic evaluation of middle and small river hydraulic engineering in the future, which provides scientific guidance for the research and application of ecological economic evaluation of hydraulic engineering.