Biodiversity and ecosystem services are the two major targets in ecological protection. Considering both biodiversity and ecosystem services in ecological protection designing will contribute to the comprehensive effects of protected area networks. In this study, biodiversity and ecosystem services, including water supply and soil retention, were evaluated in the Qinling Mountains. On the basis of these evaluations, gap analysis was carried out and a protected area network was proposed. The results showed that the current nature reserves covered 33.5% of the highly important area for biodiversity and 22.9% for water supply, but only 7.4% for soil retention. We propose to establish a protected area network that includes nature reserves and ecosystem service reserves in middle Qinling, Southwest Qinling, and Southeast Qinling. The protected area network will cover 31.4% of the entire Qinling area, and encompass a high proportion of highly important areas for biodiversity (76.2%), water supply (70.5%), and soil retention (41.5%). The results of this study will provide a basis for ecological conservation policy in these mountains, and also have implications for the establishment of protected area systems in other regions.