Dongting Lake and Poyang Lake, the China's two largest freshwater lakes, are the most important wintering area and pathways for migratory birds in East Asia. As a result of human activities (impounding of the Three Gorges Dam (TGD), and sand mining) and climate change, the dry season of Dongting Lake and Poyang Lake came early after the impoundment of TGD. And the early dry season (EDS) would change wildlife habitat and would have a negative effect on biology and biodiversity. In this paper, we compared the habitat suitability for Anatidae, Charadriidae, Ardeidae and Laridae (the four main types of migratory birds) of the Dongting Lake an d Poyang Lake between three normal hydrologic years (NY) and three hydrologic years which had EDS (EY) of each lake by geo-spatial overlay calculation, to reveal the effect of EDS on the habitat suitability for the main types of migratory birds. The grading systems of suitability included four grades: poor (0-25), fair (25-50), good (50-75), and very good (75-100). The results showed that the EDS 1) improved the habitat suitability for Anatidae; 2) had no significant influence on the habitat suitability for Charadriidae and Ardeidae; and 3) had an almost significant adverse effect (would be significant in fact and in the future) on the habitat suitability for Laridae at the two wetlands.