We investigated the distribution of Marco Polo Sheep (Ovis ammon polii) in East Pamir over a 3-year period from September 2010 to October 2013, and analyzed the habitat vegetation dynamics from 2000-2010. After defining rough survey regions by consulting the local administrative departments of wildlife conservation and pastoralists, we adopted the classical line-intercept method for on-site investigations of the distribution region and characteristics of Marco Polo Sheep. We also estimated the changes in vegetation coverage in the distribution regions of Marco Polo Sheep from 2000 to 2010 using remote sensor imaging techniques. The results showed that the Marco Polo Sheep are mainly distributed in the river valley or cleugh (3200-5200 m a.s.l.) spanning the Tashkurgan Wildlife Reserve, Bulunkou Township, Muji Township, Jigen Township, Halajun Township, and Hala Braque Township in East Pamir, and that the distribution of Marco Polo Sheep covered 47,000 km². The vegetation coverage in the Marco Polo Sheep habitat was extremely low; in 2010, vegetation covered 9.37% of the distribution of Marco Polo Sheep. Low vegetation coverage was observed for 93.80% of the total vegetation-covered area. The vegetation was seriously degenerated, and the vegetation-covered area decreased during 2000-2010 from 10382.63km² to 4444.55 km², an annual vegetation area reduction of 593.81 km². In this survey, we observed 1,611 Marco Polo Sheep, but their expected number in the region should have been 3000-3500 individuals, based on the estimated area of vegetated habitat. The Marco Polo Sheep were distributed in the Tashkurgan Wildlife Reserve at the highest density of 2.01 per km², and had a lower density in other regions. Owing to global climate change, human disturbance, overgrazing, grazing in cages, and mining, the habitat of Marco Polo Sheep has been seriously destroyed. In this paper, we suggest that a red ecological area and ecological compensation mechanism be developed, and that in-situ conservation strategies are adopted. However, we should begin to implement ex-situ conservation and in vitro protection actions, broaden the conservation strategy, and improve the effectively of protection methods.