The anti-interference ability in ecologically fragile areas is weak. It is of great significance for regional sustainable development to make clear the ecologically potential of the ecosystem and utilize resources on the basis of the potential. Based on the perspective of ecosystem service value, we attempt to measure the ecological potential of the agricultural eco-economic system. A typically representative town of three industries integration was selected as the study area to analyze the ecological potential of their agricultural eco-economic system and the leading industries in temporal and spatial aspect. Finally, the ecological functional areas were divided. The results showed that (1) the gas regulation, climate regulation, water conservation, and soil formation and protection were main service functions of the ecosystem. With the implementation of the Grain to Green program (GTGP), the ecosystem service value presented an increasing trend as the woodland became the main type of land use. There was a pattern of "middle low, side high" in spatial distribution. (2) The potential of the agricultural eco-economic system was affected by the service value and resource development process, and the potential was relatively consistent with the ecosystem service value in spatial distribution. There was a distribution pattern of "middle low and side high, high in north, and low in south". Among them, the GTGP directly led to an increasing potential of woodland, and the potential of farmland was reduced. (3) In the process of GTGP, the facility agriculture, commodity farming, forest fruit industry and service industry were formed. With the development of urban integration, the leading industry developed a trend from the extensive form to intensive mode. The tertiary industry was mainly distributed in the center of the township. The forest fruit industry was distributed in mountainous area. The facility agriculture was mainly distributed in flat area. (4) Based on the value of ecosystem services, the functional areas of agricultural eco-economic system in the study area were divided into three areas:urban eco-environment maintenance area (type I area), agricultural ecological protection area (type II area), and ecological security barrier area (type III area).