Gannan region, located in a typical hilly and mountainous area, is the state for the construction of ecological environment focused on one area. To balance the development of agricultural economic and ecological function protection, and pursues comprehensive and sustainable development, the multiple relationship between them was investigated in this paper. We proposed an agri-ecological economic index system (based on the coupling coordination degree model) to analysis coordinated development in gannan region. All the data was from 2000-2015 statistical yearbook and satellite remote sensing. The results show that:(1) the agri-ecosystem show a slightly differ between different spatial (natural conditions) except times. From 2000 to 2015, the comprehensive evaluation value of agricultural economy growth a lot with a certain spatial variation. (2) Coupling degree and coupling coordination degree increased with time, e.g. the proportion of extreme coupling increased from 0% (2000) to 94% (2015). Most counties (cities) was moderate coupling initial and growths to extreme coupling in 2015. Besides, coupling coordination degree was changed from moderate to high coupling coordination degree. In addition, a low-lying region is exhibited in middle of the study area (e.g. Yudu County, Xingguo County), and high-lying region is in northern. (3) Before 2010, most counties (cities) was in an extreme lag agricultural economy condition for a long period, meanwhile, transferring smoothly to a serious lag agricultural economy condition. The analysis of the coupling situation of agri-ecological economic system could expand our acknowledge of the development condition, evolution law of agri-ecological economic system, and promote the coordinated development of agricultural system in regions.