Abstract: Marketization and diversified ecological compensation are the supporting policies to improve the main functional zones. In this paper, a standard model of ecological compensation was established using the modified ecological footprint method. And the model of ecological compensation cost distribution among functional areas across river basins was established using the theories of ecological flow and gravitational model theory. An empirical analysis of the Dabie Mountain areas in Anhui Province was carried out using the GIS technology. The results revealed the following:1) According to the ability to pay for development areas and the ecological carrying capacity, combining the value and effect scope of ecosystem services, the ecological compensation standard, and the ecological flow coefficient provided by the protected areas, the ecological compensation model of inter-basin function area were constructed based on the environment conditions in the Dabie Mountain area. Therefore, the ecological compensation model could be scientifically adapted to the real world and could be applied to analyze spatial differentiation and quantify ecological compensation standards in the Dabie Mountain area. 2) In 2015, Jinzhai-Huoshan water source and Yuexi-Taihu-Qianshan water source had the largest ecological radiation area in the urban area of Hefei-Feixi-Feidong development zone (4 521.92 km² and 5 102.92 km², respectively), and the total value of ecological radiation of the two water sources was also the largest (36.178 2 and 38.885 million ¥, respectively). Therefore, the development zone was the main source of ecological compensation costs for the water source area. The Hefei-Feixi-Feidong development zone was close to two major agricultural producing areas, and the area affected by ecological radiation was also the largest; therefore, the value of ecological services was the largest, which was 20.982 3 million ¥ and 27.171 9 million ¥, respectively. 3) The total amount of ecological compensation provided by the four development areas was 142.439 5 million ¥, and the proportion of each area was 78.38% (Hefei Urban Region, Feidong County, and Feixi County), 9.28% (Anqing Urban Region), 9.34% (Huainan Urban Region), and 2.99% (Jin'an Region). The ecological compensation was mainly provided by Hefei City. 4) Jinzhai-Huoshan water source and Yuexi-Taihu-Qianshan water source provided ecological services valued at 57.679 7 million ¥ (accounting for 29.1%) and 58.735 2 million ¥ (accounting for 29.63%), respectively, for the development area. The surrounding main agricultural production areas also provided eco-functional services valued at 81.771 7 million ¥ (accounting for 41.26%). 5) The compensation funds provided for two water source areas were 42.367 5 million ¥ (accounting for 29.74%) and 44.245 4 million ¥ (accounting for 31.04%), respectively, and they were the main areas of compensation. The surrounding main agricultural areas also received a compensation of 55.856 6 million ¥ (accounting for 39.22%). The ecological compensation model and standard provide a scientific reference for environmental protection and construction of main functional areas.