The intensification of human activities and climate change has posed unprecedented challenges to global biodiversity and ecosystems. The loss of biodiversity can impact the functionality and stability of ecosystems, leading to a decline in the supply of ecosystem services, threatening the health and sustainability of global ecosystems. Identifying priority areas, especially areas that are crucial for biodiversity and ecosystem services is an effective way to promote successful conservation strategies and can be applied to the systematic conservation planning. Therefore, the coordination of biodiversity conservation and ecosystem services in systematic conservation planning is of great importance. The Qinghai-Tibetan Plateau, which provides various ecosystem services, serves as an ecological security barrier not only for China but also for the entire Asia. It also stands as one of the most biologically diverse regions in the world. Using the QTP as a case, this study firstly employed the Maxent model to simulate the spatial distribution of key plant species. Additionally, utilizing these modeled distribution data of plants, spatial distribution data of key animals from the IUCN and ecosystem services, we identified the individual conservation priorities of biodiversity and ecosystem services and integrated priority conservation areas considering both biodiversity and ecosystem services using Zonation model. Furthermore, we assessed the protection status and gaps of the existing protected areas (PAs) on the QTP concerning key species, ecosystem services and priority areas. The results showed that: (1) Conservation priority areas on the QTP presented a decreasing trend in conservation value from southeast to northwest, primarily located in regions like the southeastern edge of the plateau, the Himalayan mountains, the middle reaches of the Yarlung Zangbo River, and the Hengduan Mountains. There were slight differences in the distribution of areas prioritized for biodiversity conservation and ecosystem services, resulting in a 43.2% spatial overlap; (2) PAs provided the highest protection rates for amphibians (average range coverage of 38.2%), followed by mammals (24%), and reptiles with the least coverage (10.2%). Ecosystem services coverage rates were as follows: sandstorm prevention (44.1%), water retention (27.1%), soil conservation (22.3%), carbon storage (17.1%), and flood regulation (16.6%). (3) PAs covered only 26.8% of the integrated priority conservation areas, with protection gaps in levels I, II, and III priority areas accounting for 7.2%, 6.9%, and 7.7% of the QTP's total area, respectively. This study can provide scientific basis and theoretical support for the optimization of protected area system with national parks as the main component on the QTP.