Abstract: Taking 16 states and cities in Yunnan province as the research object, the evaluation index system of sustainable development of ecological economy is constructed from five aspects: economic development, ecological construction, environmental protection, resource utilization and social benefits, and their quality level of sustainable development of ecological economy is measured by entropy method. On this basis, 16 cities in the Yunnan province are divided into four types by hierarchical cluster analysis: high quality development area of ecological economy, high quality area of ecological economy development, medium quality area of ecological economic development and low quality development area of ecological economy. At the same time, the problems existing in each type of area are discussed, and the problems are given. Countermeasures and suggestions are put forward.