Black-necked crane (Grus nigricollis, BNC) is an endangered species classified as vulnerable under the revised IUCN Red List, and it faces serious threats from human activities and habitat variations. We investigated and analyzed the population and nesting microhabitat of BNCs in the Longbao National Nature Reserve (NNR) from 1978 to 2016. The number average growth rate of each decade was different, and we analyzed the reasons for the number increase from several aspects, including land cover and climate change. The establishment of the Longbao NNR represented an effective method of protecting endangered animal species. However, the land cover classification results of Landsat images showed that the marsh wetland, which is the BNC’s primary habitat, decreased, while artificial buildings, including roads and houses, increased, which affected the habitat of BNCs. The average temperature increase over the past 40 years has also had an impact on the number of BNCs. We observed 9 BNC nests, which included 5 island nests and 4 grass nests, by telescope in 2018. BNCs prefer to nest in swampy wetlands or on islands with open water or star-like distributions. The results of the principal component analysis showed that among the six microhabitat factors (elevation, habitat type, distance to roads, shortest distances to nearest water body, nearest distance between nests and disturbance), the nearest distance between nests and habitat type were the primary factors influencing nesting site selection. To promote this species, we suggest decreasing wetland fragmentation, reducing habitat degradation and providing an undisturbed habitat.