Understanding the habitat use and spatial distribution of wildlife can help conservationists determine high-priority areas and enhance conservation efforts. We studied the wintering habitat use, preference, and utilization distribution of two crane species, that is, the black-necked crane (Grus nigricollis, Przevalski, 1876) and common crane (Grus grus, Linnaeus, 1758), in Huize National Natural Reserve, Yunnan–Guizhou Plateau, southwestern China. Line transects indicated that anthropogenic farmland habitat was highly utilized and was positively selected by both crane species (>90% of flocks observed for both species). Black-necked cranes preferred marshland in spring (February and March) but avoided grassland during the entire wintering period, whereas common cranes avoided both marshland and grassland throughout the entire period. The two cranes species had communal nightly roosting sites and separate daily foraging sites. Black-necked cranes were distributed within two km (1.89 ± 0.08 km) of the roosting site, covering an area of 283.84 ha, with the core distribution area encompassing less than 100 ha. In contrast, common cranes were distributed far from the roosting site (4.38 ± 0.11 km), covering an area of 558.73 ha, with the core distribution area encompassing 224.81 ha. Thus, interspecies competition may have influenced the habitat preference and spatial distribution divergence of these two phylogenetically related species. This study should help guide habitat management as well as functional zoning development and adjustment in the future. Based on our results, we recommend restoration of additional wetlands, retention of large areas of farmland, and protection of areas that cranes use most frequently.