Sanjiangyuan National Park is the first pilot of the national park system in China. It requires the strictest ecological protection. At the same time, the relationship between the local pastoralists’ livelihood and the carrying capacity of resources and environment should be properly handled to form a new model of harmonious development between humans and nature. This study explores the nature proportion (N%), i.e., the minimum conservation area for biodiversity and ecosystem services and the maximum area for local pastoralists’ livelihood at the regional scale of the Sanjiangyuan National Park, and seeks approaches and models of sustainable management of the social-ecological system. The theoretical, realized and predicted N% are calculated based on: the diet niche volume and overlap of domestic livestock (Domestic yak and Tibetan sheep) and wild ungulate herbivores (Tibetan antelope, Tibetan gazelle, Wild yak and Tibetan wild ass), the population, density and land use of dominated livestock (116.70 × 104 sheep unit) and wild ungulate herbivores (31.40 × 104 sheep unit), and the livestock population (123.07 × 104 sheep unit) at local (6.43 × 104) pastoralists’ basic living needs, by 90%, 30 % and 74%, respectively. Furthermore, the realized and predicted N% can be optimized to 67 and 83%, respectively, by spatial coupling and optimizing of resource allocation among regions, and utilizing forage resources produced by the development of the grass industry in the peripheral support area for “Rest grazing during turning green period” and “Warm Grazing Cold Feeding Two-stage Feeding” (supplying forage for 190 days, i.e., an increase of 4.47 × 104 km2 grassland for conservation) or for livestock population
(feeding livestock of 60.25 × 104 sheep unit, i.e., increase of 1.55 × 104 km2 grassland for conservation) at local pastoralists’ basic living needs. The N% obtained by different accounting conditions, methods, and purposes is quite different. The accounting of a practical and reasonable N% under multiple targets should consider identifying, prioritizing and zoning of biodiversity conservation areas, key areas of ecological security barriers, the areas offsetting the impact of future climate change, the beneficiary areas of important ecosystem services (such as water resources), suitable areas for local pastoralists’ development, and ecosystem services assessment and quantifying of ecosystem services goods. By identifying and comprehensive consideration of all of the above factors affecting the social-ecological system, it is possible to quantify N% for Sanjiangyuan National Park at a scale of ecoregions, so as to realize its sustainable development.