The goal of “double carbon” and high-quality development put forward new requirements for green transformation in the construction industry. As an important measure to implement the concept of green and low-carbon development in the construction field, prefabricated buildings have also been applied in water conservancy projects. In order to measure the environmental-economic impact of prefabricated water conservancy projects, the concept of ecological efficiency is introduced as a measure index, and the ecological efficiency evaluation model of prefabricated concrete pump house was established based on the single ratio method, which transformed the ecological efficiency into the ratio of function, cost and carbon emission, and then the structural entropy weight method, the life cycle cost theory and the life cycle assessment method were used to build the measurement model to calculate the function, cost and carbon emission values respectively. The calculation results of the engineering example show that the ecological efficiency of prefabricated concrete pump house exceeds that of the traditional cast-in-place construction mode by 8.16%. The reason is the advantages of prefabricated water conservancy buildings in terms of construction period, quality, energy conservation and emission reduction, the prefabricated construction mode mainly dominant in terms of function and carbon emission, where the function factor is 9.64% higher and the carbon emission factor is 8.06% lower. However, due to the limitations of China’s prefabricated component production technology, the cost performance is inferior to the traditional cast-in-place construction mode. To further improve the ecological efficiency of prefabricated buildings for water conservancy projects in the future, efforts could be focused on both cost and environmental impact.