Abstract: A comprehensive evaluation system for the protection and utilization of traditional villages in Yunnan Province is built to explore how to utilize the excellent local cultural resources of traditional villages and balance their protection and utilization. The study screens indicators from the four aspects of history and culture, social culture, human settlement environment, and industrial economy, and uses the analytic hierarchy process (APH) and entropy value method to carry out the combined weight. The comprehensive evaluation system for the protection and utilization of traditional villages is constructed, including 4 first-level indicators, 9 second-level indicators, and 40 third-level indicators. An empirical study is conducted of 27 villages selected as the first and second batches of Chinese Traditional Villages in Yunnan. Firstly, the overall protection and utilization level of traditional villages in Yunnan Province is positive, and the protection effect of village resources is satisfactory, and the situation of activation utilization needs to be improved. Second, the protection of historical and cultural heritage of villages is generally ideal, as the protection level of physical cultural heritage is higher than that of intangible cultural heritage. The overall protection of human settlements is positive and the difference in scores between villages is small. The difference in scores of social governance and industrial economy is large. Thirdly, the scoring results of the traditional village protection and utilization evaluation system are summarized and analyzed, and the villages are divided into five categories.