Gut microbiota plays an important role in host metabolism, immunity, and environmental adaptation, yet its response to contrasting wintering habitats in migratory waterbirds remains poorly understood. We compared the gut microbiota of whooper swans (Cygnus cygnus) wintering in a natural riverine habitat (Swan Bay, Hejing County) and an urban wetland habitat (Worker’s Park, Korla City) in Xinjiang, China. A total of 34 fresh fecal samples were analyzed using 16S rRNA gene sequencing. We identified 2207 operational taxonomic units (OTUs), of which 734 were shared between habitats, indicating the presence of a conserved core microbiota. The urban wetland group exhibited a significantly higher Simpson index, whereas beta diversity analysis revealed significant differences in community structure between habitats (p < 0.05). Both groups were dominated by Firmicutes, Fusobacteriota, Proteobacteria, Campylobacterota, and Bacteroidota, although their relative abundances differed markedly. LEfSe analysis identified distinct habitat-associated taxa, and PICRUSt2 prediction suggested greater enrichment of metabolism-related pathways in the natural riverine group. Overall, wintering habitat was associated with differences in gut microbial composition and predicted function, providing new insight into the ecological adaptation of migratory waterbirds under contrasting environmental conditions.