The Poplar Ecological Retreat (PER) project in Dongting Lake wetland is an important measure in response to China’s ecological civilization construction policy, it aims to remove eastern cottonwoods (Populus deltoides) that artificial large-scale planted in this area and restore the natural state of the wetland, and has got a lot of attention by society and scholars. However, as one of the most important wintering place for migratory birds in the world, the impact of PER on migratory bird habitats in Dongting Lake wetland has not been evaluated. In this paper, we used the habitat suitability index model based on remote sensing to explore the impact of PER on the four mainly migratory bird guilds (Anatidae, Charadriidae, Ardeidae and Laridae) in Dongting Lake wetland. The suitability included four grades: poorly (0–25), generally (25–50), moderately (50–75), and highly (75–100). The results showed that the area of poplars in Dongting Lake wetland decreased significantly after PER was implemented. There was a negative correlation between poplar area and moderate grade habitat area of Anatidae and Ardeidae, and a positive correlation between poplar area and general grade habitat area. However, there was no significant change in different grades of habitat area of Charadriidae and Laridae after PER. Thus, PER improved the habitat suitability of Anatidae and Ardeidae, but had no significant effect on the suitability of habitat for Charadriidae and Laridae. These conclusions could provide reference for understanding the living conditions of Dongting Lake wetland waterbirds, determining the priority protection areas and maintaining wetland biodiversity.