Most migratory birds depend on stopover sites, which are essential for refueling during migration and affect their population dynamics. In the East Asian–Australasian Flyway (EAAF), however, the stopover ecology of migratory waterfowl is severely under-studied. The knowledge gaps regarding the timing, intensity and duration of stopover site usages prevent the development of effective and full annual cycle conservation strategies for migratory waterfowl in EAAF. In this study, we obtained a total of 33,493 relocations and visualized 33 completed spring migratory paths of five geese species using satellite tracking devices. We delineated 2,192,823 ha as the key stopover sites along the migration routes and found that croplands were the largest land use type within the stopover sites, followed by wetlands and natural grasslands (62.94%, 17.86% and 15.48% respectively). We further identified the conservation gaps by overlapping the stopover sites with the World Database on Protected Areas (PA). The results showed that only 15.63% (or 342,757 ha) of the stopover sites are covered by the current PA network. Our findings fulfil some key knowledge gaps for the conservation of the migratory waterbirds along the EAAF, thus enabling an integrative conservation strategy for migratory water birds in the flyway.