China is one of the world’s richest countries in terms of biodiversity, which has been seriously threatened. In 2010, to effectively protect biodiversity, the State Council of China authorized the Protection Strategy and Action Plan of China Biological Diversity (Year 2010-2030), in which 32 terrestrial Biodiversity Priority Areas were delineated as preferential areas, and background surveys of biodiversity in these areas were also discussed. To protect biodiversity, the Ministry of Environmental Protection of the People’s Republic of China, alongside various research institutions such as Chinese Academy of Sciences and universities, conducted biodiversity background surveys at the county level in 18 counties in Northwest Yunnan of the southern section of the Hengduan Mountains Area from 2010 to 2011. The survey included ecosystems and species. At the ecosystem level, the survey investigated the diversity of vegetation formations within each county. At the species level, the survey investigated diversity of species composition, quantity, and usage of higher plants, vertebrates, and macro-fungi, analyzed the quantities of endemic, rare, and endangered species. The survey culminated in a species inventory at the county level. Based on the survey results, a comparative analysis of biodiversity composition among different counties was conducted. Among the 18 investigated counties, Yulong County, Jianchuan County, Gucheng District, Shangri-La County, and Eryuan County have relatively abundant ecosystem types. While all of these counties have more than 48 formations, Yulong County has the largest number of formations (108 formations). The formations of other counties ranged from 20 to 40. Yulong County not only has the richest vegetation formations, it also has the most abundant number of species (including 4,550 higher plants, 625 vertebrates, and 222 macro-fungi). The region also has a high proportion of endemic species. With respect to higher plants, the ratio of endemic species in most of the counties is about 20%, however, the ratio can approach or exceed 50%. With respect to animal species, the ratio of endemic species in most of the counties is about 10%, with the highest ratio in Heqing County, where 46 endemic species account for 17% of the total species. The authors hold that a comprehensive biodiversity survey is a necessary basis and hence suggest that this study be taken as a case for large-scale biodiversity investigations in the future.