To solve the problem of ignoring the calculation of environment pollution in traditional ecological footprint model accounts, this paper put forward an optimized ecological footprint (EF) model, taking the pollution footprint into account. In the meantime, the environmental capacity's calculation was also added into the system of ecological capacity, and further used to do ecological assessment of Pearl River Delta urban agglomeration in 2005. The results showed a perfect inosculation between the ecological footprint and the development characteristics and spatial pattern, and illustrated that the optimized EF model could make a better orientation for the environmental pollution in the system, and also, could roundly explain the environmental effects of human activity. The optimization of ecological footprint model had better integrality and objectivity than traditional models.