Source Region of Yellow River Basin is a core zone for ecological barrier and biodiversity treasury in Tibetan Plateau. Plateau pika (Ochotona curzoniae) is widely distributed in this region and exerts profound effects on the terrestrial ecosystem. Investigating spatial distribution of pika is important to understand the role of them played in the ecosystem. In this study, we investigated pika burrow density by UAV aerial photography and field measurement in Henan county, Huangnan Prefecture, Qinghai Province, Source Region of Yellow River Basin in August 2016, August 2017, December 2017 and May 2018. Totally, 29 work points (each work ponit includes 12-16 wayponits) were set and 500 aerial photographs were obtained. Each aerial photograph taken by UAV at a height of 20 m covers approximately 35 m × 26 m ground area. We found that the distribution of pika burrows was extreme heterogeneous and unbalanced. The pika burrow density increased from 14.7 in 2016 to 20.1 per mu in 2017. We concluded that the distribution of pika burrow was regulated by the combined factors, including climate, vegetation, grazing, soil, scaffold and deratization, etc. We also analyzed the relationships of pika burrow density with the grazing intensity and the distance from water sources. The results showed that the high pika burrow density was under moderate grazing intensity and at a distance of 50 to 200 m from the water source.