The grass-livestock balance system, as a core policy tool for grassland ecological protection, has increasingly evident contradictions with the development of animal husbandry in pastoral areas. Ecological animal husbandry plays a crucial role in addressing the conflicts between protection and development. Under the constraints of grass-livestock balance, the development of ecological animal husbandry in Yushu Prefecture faces numerous structural constraints, such as reduced ecological carrying capacity, constraints from traditional concepts, feed supply shortages, low added value in the industrial chain, and a lack of relevant supporting policies. The root cause lies in the failure of collaboration among the “nature-industry-system.” This study proposes a systematic and integrated development path from three dimensions: strengthening natural foundations, enhancing industrial drivers, and improving institutional guarantees. It also demonstrates the internal mechanisms of the coordinated development paths among these three aspects, providing theoretical references for ecological protection and industrial coordinated development in ecologically fragile regions of the Qinghai-Tibet Plateau.