Livability is the organic unity of the natural eco-environment and human environment. Clarifying the livability and the hindering factors of the alpine ecological function zone on the Qinghai-Tibet Plateau is an important prerequisite for precisely improving the habitat quality and promoting the harmonious coexistence of human and nature within the ecological security barrier area. This paper is based on the fundamental paradigm of urban and rural livability evaluation, taking the uniqueness of habitat systems in alpine ecological function zone into account. From the perspective of coupling nature and humanities, a system of livability indicators for alpine ecological function areas is constructed, which consists of 4 dimensions (natural environment, living environment, facility environment, and social environment), with 8 primary indicators and 24 secondary indicators. Taking 45 counties in Qinghai Province as examples, we evaluate the livability and hindering factors quantitatively, and explore the interaction between livability and ecological importance, as well as socio-economic development status. The results show that: (1) The overall livability in Qinghai Province is low and demonstrates a decreasing geographical differentiation among Huanghe-huangshui valley ecological zone, Qaidam basin ecological zone, Qinghai lake rim ecological zone, and Three-river sources ecological zone. (2) The spatial coupling of livability and ecological importance is not coordinated, and the livability of the most important ecological zones is low. Livability is also proportional to both population size and economic development. (3) The livability of Qinghai Province is mainly hindered by the living environment and the social environment. At the eco-geographic zone layer, under the main constraints of natural factors, the Three-river sources ecological zone, the Qinghai lake rim ecological zone, and the Qaidam basin ecological zone are strongly constrained by the facilities, living, and social environment, respectively. (4) The future population guidance and habitat optimization model is proposed for the livability characteristics of different eco-geographic zones, that is, three types of spatial concentration and evacuation are defined according to livability and socio-economic-ecological gravity: population clustering type, evacuation type, and stable type. Enhance livability and spatial adaptability of population distribution through spontaneous cross-regional migration such as population urbanization, employment migration and education migration, as well as nearby ecological migration, focusing on disadvantaged areas such as the Three-river sources ecological zone and infrastructure hindering factors such as drinking water facilities, road facilities, logistics and distribution, and network communication. Thus, it will finally improve the facility configuration and supply capacity of the alpine ecological function zone habitat system.