The Tibet Autonomous Region of China constitutes a unique and fragile ecosystem that is increasingly influenced by development and global climate change. To protect biodiversity and ecosystem services in Tibet, the Chinese government established a system of nature reserves at a significant cost; however, the effectiveness of nature reserves at protecting both—biodiversity and ecosystem service functions in Tibet is not clear. To determine the success of existing nature reserves, we determined importance areas for the conservation of mammal, plant, bird, amphibian, and reptile species, and for the protection of ecosystem service functions. The results indicated that important conservation areas for endangered plants were mainly distributed in the southern part of Nyingchi City, and for endangered animals, in the southern part of Nyingchi and Shannan Cities. Extremely important conservation areas for ecosystem service functions of carbon sequestration, water and soil protection, and flood regulation were mainly distributed in the southern part of Nyingchi and Shannan Cities, northern and southeastern parts of Nagqu City, and southern part of Ngari area. Based on an analysis of spatial overlap in protection areas, we conclude that existing natural reserves need to be expanded, and new ones need to be established to better protect biodiversity in Tibet Autonomous Region.