Wind farms offer a cleaner alternative to fossil fuels and can mitigate their negative effects on climate change. However, wind farms may have negative impacts on birds. The East China Coast forms a key part of the East Asian–Australasian Flyway, and it is a crucial region for wind energy development in China. However, despite ducks being the dominant animal taxon along the East China Coast in winter and considered as particularly vulnerable to the effects of wind farms, the potential negative impacts of wind farms on duck populations remain unclear. We therefore assessed the effects of wind farms on duck abundance, distribution, and habitat use at Chongming Dongtan, which is a major wintering site for ducks along the East Asian–Australasian Flyway, using field surveys and satellite tracking. We conducted seven paired field surveys of ducks inside wind farm (IWF) and outside wind farm (OWF) sites in artificial brackish marsh, paddy fields, and aquaculture ponds. Duck abundance was significantly higher in OWF compared with IWF sites and significantly higher in artificial brackish marsh than in aquaculture ponds and paddy fields. Based on 1,918 high-resolution satellite tracking records, the main habitat types of ducks during the day and at night were artificial brackish marsh and paddy fields, respectively. Furthermore, grid-based analysis showed overlaps between ducks and wind farms, with greater overlap at night than during the day. According to resource selection functions, habitat use by wintering ducks was impacted by distance to water, land cover, human activity, and wind farm effects, and the variables predicted to have significant impacts on duck habitat use differed between day and night. Our study suggests that wintering ducks tend to avoid wind turbines at Chongming Dongtan, and landscape of paddy fields and artificial wetlands adjoining natural wetlands is crucial for wintering ducks.