Wind farms are a cleaner alternative to fossil fuels and may mitigate the effects of climate change. However, they have complex ecological consequences, especially their negative effects on birds. The East China coast is a key part of the East Asian-Australasian flyway (EAAF) for migratory waterbirds, and numerous wind farms have been or will be built in this region owing to high electricity demand and wind energy resources. However, little is known regarding the effects of large-scale wind farms of the East China coast on biodiversity conservation. The negative effects of wind farms on waterbirds that overwinter here could be reduced by understanding waterbird distribution and movement around wind turbines in these areas. From 2017 to 2019, we selected the Chongming Islands as our study area, which are one of the most important hot spots for migratory waterbirds of the East China coast and have sufficient wind generation potential to achieve energy sustainability, to study how to coordinate coastal wind farm development (existing and planned wind farms) and waterbird conservation (important waterbird habitats and buffer zone due to characteristic of waterbird activity). We identified four coastal natural wetlands of international importance for waterbirds according to 16 field surveys in 2017–2018. We found that over 63.16% species and 89.86% of waterbirds flew regularly across a dyke in Chongming Dongtan, where the wind farms are generally located, and used the natural intertidal wetland as a feeding ground and artificial habitat behind the dyke as a supplementary habitat for foraging and roosting. Additionally, with 4603 locations of 14 GPS/GSM tracked waterbirds (seven shorebirds and seven ducks) in Chongming Dongtan in 2018–2019, we further demonstrated that more than 60% of waterbird locations were within a distance of 800–1300 m from the dyke, and this distance could be defined as a buffer zone to protect waterbirds. Finally, we found that 67 existing wind turbines adjacent to four important coastal habitats on the Chongming Islands may influence waterbirds based on our finding of the buffer zone for waterbird conservation. We concluded that the settlement of wind farms should be avoided not only in important coastal natural wetlands for waterbird conservation but also in a proper buffer zone covering the artificial wetlands, such as aquaculture ponds and paddy fields adjoining these important natural wetlands.