The red-crowned crane (Grus japonensis (Statius Müller, 1776)) is a rare and endangered species that lives in wetlands. In this study, we used variance partitioning and hierarchical partitioning methods to explore the red-crowned crane-habitat relationship at multiple scales in the Yellow River Delta Nature Reserve (YRDNR). In addition, we used habitat modeling to identify the cranes' habitat distribution pattern and protection gaps in the YRDNR. The variance partitioning results showed that habitat variables accounted for a substantially larger total and pure variation in crane occupancy than the variation accounted for by spatial variables at the first level. Landscape factors had the largest total (45.13%) and independent effects (17.42%) at the second level. The hierarchical partitioning results showed that the percentage of seepweed tidal flats were the main limiting factor at the landscape scale. Vegetation coverage contributed the greatest independent explanatory power at the plot scale, and patch area was the predominant factor at the patch scale. Our habitat modeling results showed that crane suitable habitat covered more than 26% of the reserve area and that there remained a large protection gap with an area of 20,455 ha, which accounted for 69.51% of the total suitable habitat of cranes. Our study indicates that landscape and plot factors make a relatively large contribution to crane occupancy and that the focus of conservation effects should be directed toward landscape- and plot-level factors by enhancing the protection of seepweed tidal flats, tamarisk-seepweed tidal flats, reed marshes and other natural wetlands. We propose that efforts should be made to strengthen wetland restoration, adjust functional zoning maps, and improve the management of human disturbance in the YRDNR.