Abstract: With the promotion of new urbanization and ecological construction, the objective and quantitative evaluation of the status of regional eco-environment is one of the most important and is the urgent tasks of the ecological construction at the current stage. High-density human activities can exert excessive pressure on natural eco-system. The analysis of the ecological carrying capacity can measure such impact quantitatively, and provide a reference for regional sustainable development. This paper mainly calculated the ecological footprint and ecological carrying capacity of counties in Wuhan urban agglomeration in 2008 and 2013 on the basis of the ecological footprint pattern, and analyzed the temporal and spatial variations. It was discovered that the ecological footprint and ecological carrying capacity of the counties in the urban agglomeration were significant difference in space, the ecological footprint increased with the passage of time, while the carrying capacity varied slightly, presenting a polarized phenomenon. According to the ecological footprint calculation results, we establish spatial transfer Ecological compensation among districts in Wuhan urban agglomeration. Having calculated the ecological compensation across different districts based on the ecological footprint and ecological carrying capacity, this paper performed the transfer payments in 2008 and 2013 of Wuhan urban agglomeration. The results indicated that if the financial transfer payment is carried out, the whole districts could form a balance of supply and demand in the ecological system, alleviate the ecological pressure of Wuhan urban agglomeration, and realize the sustainable development of Wuhan urban agglomeration.