Millions of migratory waterfowl winter in the coastal wetlands in Shanghai City, among which Eastern Spot-billed Ducks and Mallards are among the most common species and are sensitive to infection with avian influenza virus. However, information on the migration behaviors of these two species in Northeast Asia is lacking. Therefore, GPS transmitters were used to track the migration of 13 Eastern Spot-billed Ducks and eight Mallards wintering in Shanghai during 2017–2020. Mallards covered a (mean ± standard deviation) migration distance of 1,663.69 ± 1,063.33 km, with wider variation than Eastern Spot-billed Ducks (1,639.24 ± 642.72 km), though the difference was not significant. Both species ended their northward migrations in Northeast Asia encircling the Yellow Sea, mainly in northeastern China. The dynamic Brownian bridge movement model confirmed that multiple stopover sites mainly located in the Korean Peninsula along the Yellow Sea coastline were crucial nodes for maintaining the stability and function of the migration network. This study confirmed the close relationships between habitats in the Korean Peninsula and China, indicating the importance of habitat conservation in related countries to the stability of the migration network. The results of this study additionally highlight the relationships between migration behaviors and outbreaks of avian influenza virus in Northeast Asia.