Biodiversity losing and unreasonable use of nature resources are two important environmental issues. In order to protect biodiversity rescources, many countries have established numerous nature reserves and other types of protected areas. However, degradation of natural resources is a big challenge in conservation projects, and we cannot prohibit all the activities associated with economic development in the conserved areas, particularly in southwest China. There is a serious conflict between two aspects. One aspect is the rich biodiversity, increasing its importance for conservation. The other is the backward economy that requires more resources for local development. Therefore, land zoning is an important approach that can reduce conflict by partitioning the landscape into various land use units that are managed according to different levels of human activity. Our research focuses on the Three Parallel Rivers of the Yunnan Protected Area. We present a systematic methodology that integrates vegetation plot data with Geographic Information Systems (GIS) using a multi-criteria decision analysis (MCDA) technique to guide a zoning scheme. The vegetation plot data include species richness, rarity of vegetation, number of endangered plant species, ranking of endangered species, and quality of habitat. Based on these data, the protection value scores for the sub-vegetation in northwest Yunnan were obtained. Then altitude, distance to villages, distance to roads and distance to rivers were used as the impact factors to simulate the pattern of protection cost. The protection value and protection cost were integrated to generate a final combined suitability map. A K-means cluster analysis was performed to classify the suitability map into four priority levels. In this study, the area considered under level 1 was 16983 km², accounting for 25.58% of the total research area. The targeted areas for protection in level 1 included sub-vegetation of monsoon evergreen broad-leaved forest, cold-temperate coniferous forest, alpine and sub-alpine meadow, cold-temperate shrub, and areas covered by snow and water; level 1 accounts for the most important protection areas where important forest ecosystems, grassland ecosystems, and wetland ecosystems can be found. The areas under level 1 can be further divided into six parts. Part 1 is located northeast of Zhongdian; the average altitude is above 3000 m, and it is covered by cold-temperate coniferous forest. Part 2 comprises most areas of Denqing and northern Weixi, which include the Meili and Baima snowmountains. Part 3 forms the main part of the Nu mountains in Yunnan, and it appears as a line. Part 4 is located in Gongshan and Fugong, including the main part of Gaoligong National Nature Reserve. Part 5 comprises regions of southeast Zhongdian, northwest Ninglang, and northeast Lijiang. Although this part has a large area, its distribution is scattered. Part 6 comprises the Erhai Lake in Dali, which has a small area, and it is the only critical conservation region southeast of our research area. Level 2 accounts for the main areas for the conservation of forest ecosystems. Therefore, we suggested that an equal protection effort as level 1 should be made. Level 3 had a low protection value and we could use it as a buffer zone. Level 4 had no protection value and was considered the traditional land use area. According to the priority levels, we determined the area under level 1 as the priority area. We believe that our results will be useful as a reference for extension of reserves in northwest Yunnan in the future.