Effective conservation measures largely depend on knowledge of habitat selection of target species. Little is known about the scale characteristics and temporal rhythm of habitat selection of the endangered red-crowned crane, limiting the habitat conservation. Here, two red-crowned cranes were tracked with Global position system (GPS) for two years in Yancheng National Nature Reserve (YNNR). A multiscale approach was developed to identify the spatiotemporal pattern of habitat selection of red-crowned cranes. The results revealed that Red-crowned cranes preferred to select Scirpus mariqueter, ponds, Suaeda salsa, and Phragmites australis, and avoid Spartina alterniflora. In each season, habitat selection ratio for Scirpus mariqueter and ponds was the highest during the day and night, respectively. Further multiscale analysis showed that the percent coverage of Scirpus mariqueter at the 200-m to 500-m scale was the most important predictor for all habitat selection modeling, emphasizing the importance of restoring a large area of Scirpus mariqueter habitat for red-crowned crane population restoration. Additionally, other variables affect habitat selection at different scales, and their contributions vary with seasonal and circadian rhythm. Furthermore, habitat suitability was mapped to provide a direct basis for habitat management. The suitable area of daytime and nighttime habitat accounted for 5.4%–19.0% and 4.6%–10.2% of the study area, respectively, implying the urgency of restoration. The study highlighted the scale and temporal rhythms of habitat selection for various endangered species that depend on small habitats. The proposed multiscale approach applies to the restoration and management of habitats of various endangered species.