The core zone of the Yancheng National Natural Reserve (YNNR) in China is the largest wintering habitat of red-crowned cranes (cranes) in the world. However, the invasion of Spartina alterniflora (S. alterniflora) not only changed the original landscape structure of the wetlands but also impacted the cranes' habitats in the YNNR. In this paper, field investigation data and landscape pattern indices were used to analyze the effects of the S. alterniflora invasion on the habitat quality of wintering cranes. The results indicate that the seep weed (Suaeda salsa) in the natural wetland and the common reed (Phragmites australis) in the managed wetland both provide suitable habitats for cranes. However, the cranes prefer the natural wetland more. The explosive growth of S. alterniflora in the natural area has led to a significant reduction of the cranes' habitat. The area of crane habitat decreased from 52.07 km2 in 2000 to 22.36 km2 in 2015. As a result of the S. alterniflora invasion, the benthic biomass has declined, which has negatively impacted the quantity and structure of the food utilized by the cranes. This study has both theoretical and practical significance and provides a scientific basis for protecting the wintering habitat of the red-crowned cranes.