Ecological footprint theory and its application achievements in global and regional sustainable development system are studied,finding that the application of ecological footprint theory to regional sustainability evaluation leads to a perplexity that the indicated result is inconsistent with the philosophy of sustainable development theory.It is thought that the reason of the perplexity is that the ecological footprint theory based on global ecosystem is improperly adopted in regional sustainable development system, and the essential one is the faulty of the ecological footprint theory.A modification on this theory is made by introducing consumptive ecological footprint and productive ecological footprint, in which the latter is taken as the indicator of regional sustainability.The development impartiality can be demonstrated by comparison between the globe ecological deficit per capita and regional consumptive ecological deficit per capita.