In minority areas of Yunnan, China, the ecological environment is fragile, and social and economic development is not sufficient. The research on the evolution of human-earth systems can provide scientific guidance for solving the contradiction between environmental protection and social and economic development and promoting high-quality regional development. In this study, based on the structural division of the human-earth system, we established a comprehensive evaluation model by the data envelopment analysis (DEA) to analyze the evolution characteristics and influencing factors of the man-earth system in minority areas of Yunnan in terms of the coordinated development degree and the comprehensive efficiency of the system. The results show that: (1) From 1995 to 2020, the coordinated development degree of the human-earth system in minority areas of Yunnan showed an overall upward trend, with the average value rising from 0.31 in 1995 to 0.74 in 2020. (2) The average comprehensive efficiency of inputs and outputs of the human-earth system showed a downward trend; in particular, after 2007, the number of regions with ineffective DEA gradually increased, indicating that the development model of high inputs and consumption has not been effectively changed. (3) By calculating the system indicator weights using the entropy method, we found that the comprehensive utilization rate of industrial solid waste, total foreign trade and urbanization rate greatly impacted the coordinated development efficiency of the human-earth system in minority areas of Yunnan.