The East Asian–Australasian Flyway (EAAF) is experiencing notable population declines in its migratory waterbird species. Understanding the foraging ecology of these waterbirds, including ducks, is crucial for monitoring and safeguarding their food sources and wetland habitats. Here, we used a DNA metabarcoding approach to analyze fecal DNA from duck species to elucidate their dietary composition during the wintering period in a subtropical East Asian wetland. By employing multiple markers (18S, COI, and trnL) targeting different taxonomic groups and levels, we offered a comprehensive dietary analysis for omnivores that consume both plants and animals. We revealed the dietary compositions of common migratory duck species and their intraspecific and interspecific dietary variations. While ducks are generally known to be omnivorous, Anas crecca (green‐winged teal) had a more specialized diet and was primarily herbivorous throughout winter. In contrast, the sympatric Mareca penelope (Eurasian wigeon) and Spatula clypeata (northern shoveler) exhibited more omnivorous foraging behaviors. Moreover, A. crecca displayed less dietary variation among samples, while samples of M. penelope and S. clypeata were highly variable in their compositions. Comparing our results with those of studies conducted in different regions, we found that the dietary compositions of these duck species varied to different degrees across geographic locations. This variation underscores the flexibility of these duck species in their diets and their adaptable foraging strategies. Our findings also indicate that grasslands rich in herbaceous plants and aquatic environments abundant with small aquatic invertebrates are vital foraging habitats for duck species during their winter period.