The construction of inter-basin water diversion projects is one of the most effective measures targeting the uneven spatial and temporal distribution of water resources and the imbalance of social water demands. An inter-basin water diversion project involves in multiple different basins, it has complicated structures with multi-functional purposes, and always intersects with local reservoirs, lakes, channels or other water transport systems. Based on these characteristics, we adopted the energy analysis method, which considers the ecological value as vital as economic value, to quantitatively analyze the ecological benefits of East Zhejiang Water Diversion Project for the ecological environment of the areas along the route. The results show that this quantification method can be applied to the calculation of ecological benefits of actual diversion projects, and its results are more accurate and closer to the actual situation than those of the commonly used equivalent substitution method in the past.