The Black-necked Crane (Grus nigricollis) is the endemic species of the Qinghai-Tibetan Plateau, and the population in Xinjiang is mainly distributed in the regions of Pamir, Karakorum, Kunlun and Altun Mountains. A survey on the distribution, population size, population fluctuation, behavior character, breeding ecology and conservation strategy was conducted from 2010 to 2013. Population size and distribution in this area was investigated with direct count methods. At a total of 25 sampling sites, 164 observations were made during this period. We found 173 Black-necked Cranes on the wetlands of Wuzunxiaoer, Tiemulike, Yusup Aleksei, Yaziquan, Qimantag, Tula Ranch and so on. 126 individuals were recorded in the Yixiekepati wetlands (N37°15'-37°23',E90°11'-90°20', elevation 3,903 m), which is the largest population we have observed in this area. Combined with the previous records, we concluded that there are about 220-260 individuals of Black-necked Cranes in this region. The population size was estimated of 300-380 individuals in the whole Xinjiang. The numbers of family members varied from one to four, and those four types of families accounted for 5.9%, 60.3%, 29.4% and 4.4% of the records respectively. Before October, the cranes moved in single families, and they did not join other family groups. Cranes gathered in the middle of October and the highest numbers appeared on 29 October. All of the cranes migrated out of this area by 6 November. In addition, we found Eurasian Crane (Grus grus), Demoiselle Crane (Anthropoides virgo), Bar-headed Goose (Anser indicus), Greylag Goose (Anser anser) and Ruddy Shelduck (Tadorna ferruginea) in this area. According to our field work and preliminary interviews, we found that because of environmental changes, the increase of livestock husbandry, mining and eco-tourism, the population of Black-necked Cranes has faced threats in recent years. Increasing livestock husbandry, mining and eco-tourism activities potentially threaten Black-necked Cranes with poaching and egg-collection. In response to these threats, the protection and management work of the reserve administration needs to be strengthened, and herders, miners, tourist and reserve staff all need to be educated about the protected status of cranes. At the same time, a long-term monitoring program should be established to strengthen the conservation and management of Black-necked Cranes in the reserve. The number of juveniles that we observed (16.5%, n=158) can be used as a baseline to monitor future fecundity and population trends.