With the acceleration of China's urbanization process, the ecological problems are becoming more and more serious, and the contradiction between development and protection is becoming more and more prominent. How to objectively and quantitatively compensate the damaged areas, and balance development and environmental health is one of the important tasks in the ecological construction. This paper took 19 provincially administrative regions in the Yangtze River Basin as the research object, based on the "provincial hectare" model, modified the equilibrium factor and yield factor, calculated the ecological footprint and ecological carrying capacity, and made spatial analysis by GIS. At the same time, combined with ecosystem service value, a dynamic ecological compensation standard model of the Yangtze River Basin was established. The amount of ecological compensation in each administrative region was calculated, and the differentiation analysis was carried out at the watershed scale, urban agglomeration scale and provincial scale. The results show that:(1) there was no significant change in the ecological footprint and ecological carrying capacity of the Yangtze River Basin from 2015 to 2017. The ecological security indexes of provincial administrative regions are greater than 1, indicating that the whole basin is in an unsafe state and needs to be compensated. (2) For the whole Yangtze River Basin, the ecological compensation amount averaged 116.91 billion CNY in three years. (3) On the watershed scale, the ecological compensation amount in the upper, middle and lower reaches shows a gradually increasing trend. On the scale of urban agglomeration, the ecological compensation amount of Chengdu-Chongqing urban agglomeration is the lowest and the Yangtze River Delta urban agglomeration is the highest. On the provincial scale, the ecological compensation amount of Shanghai is the highest and Tibet is the lowest. The ecological security index calculated by ecological footprint and ecological carrying capacity can quantitatively compensate and analyze the state of ecological environment, and provide guiding suggestions for the determination of ecological compensation area.