Ongoing wind energy developments play a key role in mitigating the global effects of climate change and the energy crisis; however, they have complex ecological consequences for many flying animals. The Yellow Sea coast is considered as an ecological bottleneck for migratory waterbirds along the East Asian–Australasian flyway (EAAF), and is also an important wind farm base in China. However, the effects of large-scale onshore wind farms along the EAAF on multidimensional waterbird diversity, and how to mitigate these effects, remain unclear. Here we examined how wind farms and their surrounding landscapes affected multidimensional waterbird diversity along the Yellow Sea coast. Taxonomic, functional, and phylogenetic diversity of the waterbird assemblages, and mean pairwise distances and nearest taxon distances with null models were quantified in relation to four different wind turbine densities. We also measured six landscape variables. Multi-dimensional waterbird diversity (taxonomic, functional, and phylogenetic diversity) significantly decreased with increasing wind turbine density. Functional and phylogenetic structures tended to be clustered in waterbird communities, and environmental filtering drove waterbird community assemblages. Furthermore, waterbird diversity was regulated by a combination of wind turbine density and landscape variables, with edge density of aquaculture ponds, in addition to wind turbine density, having the greatest independent contribution to waterbird diversity. These results suggest that attempts to mitigate the impact of wind farms on waterbird diversity could involve the landscape transformation of wind farm regions, e.g., by including high-edge-density aquaculture ponds (i.e. industrial ponds) around wind farms, instead of traditional low-edge-density aquaculture ponds.