The red-crowned crane (Grus japonensis), a globally endangered species, is under first-grade state protection in China. There are about 3050 individuals of wild red-crowned crane in the world. Recently, the western flyway subpopulation of red-crowned crane has sharply decreased. Previous studies have primarily focused on population size, distribution and habitat selection of red-crowned crane, and several studies have further examined the effects of human disturbance on these factors. However, the majority of such studies concentrated on the coastal regions of Yancheng, Jiangsu Province, over short time; few studies focus on historical tracking of wintering red-crowned crane populations and wintering behaviors over long time. Using trace data and land-use data available over a comparatively long period, the study systematically analyzed the dynamic changes in population size and habitats distribution of wintering red-crowned crane since 1982. Thus the study reveals the effects of land use changes to the wintering habitats of the red-crowned crane. These results can include three conclusions. First, the population of wintering red-crowned crane has changed substantially from 1982 to 2015; the current population size is 50% lower than that recorded in the 1990s. Second, the range of wintering habitats has gradually reduced, and the remaining habitats have been severely fragmented. The red-crowned crane prefers various types of wetlands in winter. During the 1980s, the red-crowned crane was widely distributed in the northern Jiangsu, particularly in the swamps around island lakes in the middle and lower reaches of the Yangtze River, as well as in the coastal wetlands of Jiangsu. Over following decades, wintering habitats gradually shifted to coastal areas, primarily distributed in Sheyang County, Yancheng. However, with increasing development of the coastal economy at the beginning of the twenty-first century, wintering habitats in coastal areas were further reduced and fragmented. At present, wintering red-crowned cranes are concentrated in the central area of the Yancheng National Nature Reserve. Third, according to the Pearson correlation analysis, the habitat distribution points of wintering red-crowned crane are significantly related with the land use types and the socio-economic development. The rapid development of the Chinese economy, accompanied by the rapid expansion of land use for construction and industry directly decreased the area of habitat of wintering red-crowned crane. Additionally, changes in the distribution and intensity of land use and human disturbance caused existing habitats to be fragmented, reducing their suitability for use as of wintering habitats by red-crowned crane.