The wild large herbivores inhabiting the Yellow-River-Source National Park (YRSNP) are confronted with a significant threat from climate change and human activities. In response to these detrimental influences, measures have been proposed by the government, such as the Ecological Conservation and Restoration Project in the Sanjiangyuan Region (ECRPSR) and the establishment of the Sanjiangyuan National Park (SNP). To advance species diversity, it is crucial to investigate the spatial distribution of large herbivores, identify factors influencing their distribution, and address conflicts arising from divergent plans within the YRSNP. In this study, unmanned aerial vehicles were employed for surveying the distribution of the Tibetan wild ass (Equus kiang) and Tibetan gazelle (Procapra picticaudata). The findings indicate that the optimal habitat area for Tibetan wild ass is 437.16 km2, while for Tibetan gazelle, it is 776.46 km2. Precipitation and the human footprint index emerge as the primary factors influencing the habitat distribution of large herbivores within the YRSNP. Under the influence of the ECRPSR, there was a noteworthy expansion of the habitat area for Tibetan wild ass by 791.25 km2, and for Tibetan gazelle, it expanded by 1612.94 km2. From a wildlife conservation standpoint, this study proposes the establishment of a wildlife refuge in the YRSNP, effective coordination of conflicts between various functional zones and plans, preservation of suitable habitats for large herbivores, and the provision of a scientific foundation to reconcile development and conservation conflicts in the region, while concurrently fostering biodiversity conservation.