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Simple Summary: The black-necked crane is the only crane species that breeds on the Qinghai–Tibetan plateau, and habitat destruction and loss are the major threats to it. The Shaluli Mountains, located in a biological hotspot, is an important breeding site for the central population of the black-necked crane, but its population size and distribution, as well as shifts in distribution under climatic change, remain unknown. Therefore, we conducted a field survey and modeled the breeding black-necked crane habitat with a species distribution model in the region. The results showed that the number of breeding black-necked cranes in the area was about 200, and they were mainly distributed in a gentle meadow and wetland along the lake. Climate change will increase the potentially suitable habitat area, with a trend of northwestward expansion and upward migration, as well as an increase in habitat suitability and connectivity. In addition, more conservation gaps will arise, but the conservation role of existing protected areas will not decline. Therefore, we suggest strengthening the long-term monitoring of black-necked cranes and wetland resources in this area. Climate change is affecting biodiversity by altering the geographical distribution range of species, and this effect is amplified in climate-sensitive areas. Studying the geographic distribution of flagship species in response to climate change is important for the long-term conservation of species and the maintenance of regional biodiversity. Therefore, we collected field survey records from 2016 to 2020 and conducted field surveys of black-necked cranes in the Shaluli Mountains (SLLMs) in May–June and August–October 2021; 103 breeding records were acquired totally, and the geographical distribution range under the current and four future climate scenarios was modeled with the MaxEnt model to predict the impact of climate change on its distribution and habitat quality. The results showed that 152 black-necked cranes were surveyed in seven counties of SLLMs in total; the estimated number of black-necked cranes in the entire SLLMs was about 200. The currently suitable habitat area is 27,122 km2, mainly distributed in gentle meadows and wetland habitats along the lake where the Annual Mean Temperature is −1 °C and the Mean Diurnal Range (16 °C) and Precipitation Seasonality (105) are comparatively large. Furthermore, the breeding range would expand to varying degrees under future climate scenarios and showed a migration trend toward the northwest and higher elevation. Besides, as time goes by, the habitat for black-necked cranes in SLLMs would become more homogeneous and more suitable. The conservation effectiveness of the existing reserve network would keep stable with climate change, although there are large conservation gaps between protected areas, and these gaps will gradually expand over time. Overall, this study provides a preliminary understanding of the population and distribution and predicts the future distribution of black-necked cranes in the SLLMs. It also demonstrates the importance of SLLMs for protecting the central population of black-necked cranes and maintaining regional biodiversity. Therefore, we recommend long-term monitoring and conservation of the black-necked crane population and wetland resources in the region. [ABSTRACT FROM AUTHOR]