As hydropower project construction and ecological support systems become more interdependent, new disciplines are needed to assess this ecological effect. An ecological footprint model of the hydropower project is presented based on the emergy theory (Em-EF). Modifications have been made to the Em-EF model, in response to its perceived shortcomings. The emergy of additional capacity of reservoir should be included in the renewable natural resources account. Further, the same emergy density should be used to calculate the ecological capacity supplied account and the ecological footprint occupied account. The aim of this paper is to show a modified ecological footprint calculation for the hydropower project. A large-scale (Ⅱ) hydropower project is selected as an example for the application. To demonstrate the mechanics of this modified method, we compared our calculations with the conventional one. The same conclusion is drawn using both methods: the ecological deficit of the hydropower project will occur before the design equilibrium year. But, the needed time to offset the ecological deficit is different. The modified model gives an even rational result than the conventional one.