The wild yak (Bos mutus) is an endemic and flagship species on the Qinghai-Tibetan Plateau (QTP) of China. Because this is an aggressive and huge ungulate living in the Altun National Nature Reserve (ANNR), monitoring and surveying of wild yaks at a close distance is very difficult. An Unmanned Aerial Vehicle (UAV) offers a useful and effective tool to monitor and survey wild yaks. We used this approach in the Kumkury Desert of the ANNR, which is the highest desert in the world. The results showed that the proportion of (1) adult bulls, (2) young bulls and adult cows, and (3) calves was 1:10:5. The slopes traversed (0°–28°) within habitats and between two major habitats was higher than those (1°–13°) between habitats and water bodies, and between water bodies and food areas (alpine wet meadow in the north). There were five movement routes from rest habitats to food areas. Moreover, vehicle tracks disrupted yak migration routes from two major habitats to food areas. In conclusion, a UAV is a new multi-purpose monitoring approach for surveying large wildlife and their habitats in remote and very sparsely populated areas, and for identifying human disturbances. Using a UAV can capture detailed data on animal movements for scientific researchers. A UAV can patrol a large area that is hard to reach and provide information quickly; it can also reduce the costs of daily patrolling to determine movements.