Coastal wetlands are of great importance for biodiversity conservation as wintering, stop-over, and breeding sites for migratory waterbirds. Assessment on habitat suitability provides a scientific basis for the rational planning and management of waterbirds habitats. In this paper, urban wetlands in Shenzhen Bay and rural wetlands in Leizhou Bay were selected as the study areas. High-resolution remote sensing images were used to extract the habitat types of waterbirds. The assessment factors and their weights were determined by analytic hierarchy process (AHP). According to the main ecological factors such as food, moisture, and human disturbances, the suitability of each habitat was graded. The study compared the differences in the spatio-temporal distribution of habitat suitability of migratory waterbirds from 2010 to 2019. Based on the analysis of the driving forces, recommendations for migratory waterbird habitat conservation were proposed. The results show that:(1) from 2010 to 2019, 193.4 hm² strong disturbance areas were transformed into medium and weak disturbance areas in Shenzhen Bay, while 16.36 hm² medium disturbance areas were transformed into weak and no disturbance areas in Leizhou Bay. (2) The Shenzhen Bay was dominated by medium suitable habitats, with 83.74% and 88.71% of the total area in 2010 and 2019; while the Leizhou Bay was mainly dominated by sub-suitable and medium suitable habitats, with 86.72% of the total area in 2010 and less variation in 2019. The overall suitability of Leizhou Bay was higher than that of Shenzhen Bay. (3) The unsuitable and sub-suitable habitats in Shenzhen Bay decreased by 245.54 hm² and 26.37 hm² from 2010 to 2019, which were transformed into moderate suitable habitats; while 24.31 hm² moderate and sub-suitable areas were transformed into suitable habitats in Leizhou Bay.