The establishment of nature reserves is the most effective and basic measure to protect and maintain biodiversity. Under limited capital and manpower conditions, how to refer the different human interference protect priority construction area and select the appropriate protection plan has always been the focus of debate among conservation biologists. Taking the southern section of Hengduan Mountain as an example, this study focuses on the different levels of human disturbance during the construction of the protected area, take the high and low levels of human disturbance as the starting point, based on the principles and methods of Multi-criteria decision analysis, and based on the vegetation ecosystem and human disturbance intensity factors in the southern section of Hengduan Mountain, and comparative analysis of ecological system protection value distribution, human disturbance pattern and protection effectiveness in the southern section of Hengduan Mountain. The results showed that:First, the area of forest ecosystem (coniferous and broad-leaved mixed forest, evergreen broad-leaved forest, deciduous broad-leaved forest, deciduous mixed forest, evergreen coniferous forest), wetland ecosystem (lakes, rivers, herbaceous wetlands), alpine ecosystems (glaciers and permanent snow, alpine meadows, alpine grasslands) are of high value and score higher than 21 points; Second, the analysis of the high and low levels of human interference,based on the perspective of maintaining and improving regional biodiversity, and put forward different protection priority areas and protection strategies.Third, the protection priority areas identified in the southern section of Hengduan Mountain mainly include Ebian County, Mabian County, Shimian County, Yuexi County, Baoshan City, Tengchong City, Weixi County, Deqin County, Chayu County and other areas.