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This paper analyzes the structure of Yunnan higher education in the sight of ecology, The Purposes is to find out the regional differences of Yunnan higher education is extremely obvious on the layout and hier-archy structure; Through the analysis and comparison the regional differences of Yunnan higher education on the layout and hierarchy structure, I’ve come to the conclusion that higher education between region and intra-regional keep highly collaboration on the social economic environment. It belongs to the population of optimization distribution and shows material exchange of energy balance in the mass.