Equilibrium of the grassland yield, livestock carrying capacity, and animal husbandry population is the key factor that influences the ecological environment and sustainable development in pastoral areas. It is of great importance to define the animal husbandry pressure and carrying capacity of an animal husbandry population for grassland management policy-making and the sustainable development of animal husbandry. As one of the areas with the most sensitive and vulnerable ecosystem in China, the Three-River Headwaters Region is an ecological barrier for the environmental security and regional sustainable development of Southeast Asian nations. It is of great significance to define the livestock carrying capacity and population pressure in the area. This research estimates the net primary productivity (NPP) of vegetation in the Three-River Headwaters Region using Carnegie-Ames-Stanford approach (CASA) model, estimates the grass yield on the basis of NPP data, and then estimates the reasonable livestock carrying capacity according to the grass yield. Meanwhile, combined with herdsmen investigation data, it establishes a quantitative relationship between the proper livestock carrying capacity and reasonable animal husbandry population. In addition, the spatial distribution of an overloading animal husbandry population is analyzed through spatial interpolation, which can provide theoretical support for the establishment of scientific ecological immigration policy and the sustainable development of local animal husbandry. The results show that (1) the total grass yield of the grassland in the Three-River Headwaters Region is 13.96 million tons, and the average grass yield is 529.87 kg/hm2, whilst the spatial distribution presents a decreasing trend from the east and southeast to the west and northwest; (2) the reasonable livestock carrying capacity is 14.03 million sheep units (hereinafter referred as “SU”), and the average livestock carrying capacity is 55.14 SU/km2; and (3) the reasonable animal husbandry population carrying capacity is 512,500 people, while the actual amount is 645,300, with 132,800 people beyond the carrying capacity, especially in Xinghai, Tongde, Zekog, Yushu, Nangqen, and Chindu County.