Climate change impacts bird migration phenology, causing changes in departure and arrival dates, leading to potential mismatches between migration and other key seasonal constraints. While the impacts of climate change on arrival at breeding grounds have been relatively well documented, little is known about the impacts of climate change on post-breeding migration, especially at stopover sites. Here we use long-term (11 years) banding data (11,118 captures) from 7 species at Mai Po Marshes Nature Reserve in Hong Kong, a key stopover site for migratory birds along the East Asian–Australasian Flyway, to describe long-term changes in migration phenology and to compare observed changes to annual weather variation. We also examine changes in wing length over a longer time period (1985–2020) as wing length often correlates positively with migration distance. We found that observed changes in migratory phenology vary by species; three species had later estimated arrival (by 1.8 days per year), peak (by 2.6 days per year) or departure (by 2.5 days per year), one showed an earlier peak date (by 1.8 days per year) and two showed longer duration of passage (2.7 days longer and 3.2 days longer per year). Three species exhibited no long-term change in migration phenology. For two of the four species with shifting phenology, temperature was an important predictor of changing peak date, departure dates and duration of passage. Wing length was shorter in three species and longer in two species, but these changes did not correlate with observed phenological changes. The complex changes observed here are indicative of the challenges concerning the detection of climate change in migratory stopover sites. Continued monitoring and a better understanding of the dynamics of all sites in the migratory pathway will aid conservation of these species under global change.