Abstract: To resolve the dual contradiction between agricultural economic growth and ecological protection in Yunnan and provide a reference for the coordinated development of mountainous and border agricultural areas, this study took 16 prefectures and cities in Yunnan Province from 2014 to 2023 as research units, constructed a comprehensive evaluation system for the dual systems of agricultural economy and ecological environment, and used the entropy weight method, coupling coordination degree model, grey correlation analysis and obstacle degree model to systematically analyze the spatio-temporal evolution law, core driving factors and regional heterogeneous obstacle factors of the coordinated development of the two systems. The results showed that Yunnan's agricultural economy system had an average annual growth of 40.12% and the ecological environment system 8.39%, with a natural tension in the growth of the two systems; the coupling coordination degree achieved a five-level leap, and the pattern of high-quality coordination across the whole province was basically formed in 2023; the urbanization rate and per capita disposable income of rural residents were the core driving factors, with grey correlation degrees of 0.837 and 0.739 respectively; the restrictive factors shifted from the production side to the resource and environment side, with the obstacle degree of water resource utilization reaching 44.23% in 2023. There were significant regional differences in obstacle factors between prefecture-level cities and autonomous prefectures, and border autonomous prefectures faced more complex contradictions between development and protection. The research provides theoretical support and practical reference for the in-depth coordinated development of agricultural economy and ecological environment in Yunnan and similar regions.