The ecological compensation has been a widely concerned hot issue in recent years,and reasonable allocation of the compensation is an important content as for the regional coordinated development.By using AHP(analytic hierarchy process)and GIS with the statistical information which related to the ecological compensation,the paper established a system of compensation index with each given weight,set up the allocation framework with GIS,calculated and expressed the regional compensation value.The study showed that when allocating the ecological compensation in Lu'an City,the ecological environment,resources and economic development accounted for more weight than social equality,technical level and environmental management.Based on the total sum of ecological compensation of RMB 7.338billion yuan from the actual situation of water and carbon emission in Lu'an City,the value of ecological compensation for every administration allocated by appling the allocation model was 0.496 9billion yuan in Lu'an City,0.770 5billion yuan in Shouxian Conuty,0.917 2billion yuan in Huqiu Conuty,0.953 9billion yuan in Shucheng Conuty,2.832 5 billion yuan in Jinzai Conuty and 1.394 2billion yuan in Huoshan Conuty.