Abstract: The Yellow River Estuary hosts China′s most representative warm-temperate estuarine wetland ecosystem and serves as an irreplaceable key node on international bird migration routes. Currently, the Yellow River Estuary is preparing to establish a national park. National parks represent the protected area category with the highest ecological value and the strongest conservation intensity in China. To support seasonally differentiated management within national park and enhance conservation outcomes for migratory birds, this study focused on swan geese (Anser cygnoides), integrating satellite tracking data with field observation counts to construct an integrated species distribution model. The study analyzed the spatiotemporal dynamics of swan geese within the Yellow River Estuary National Park Candidate Area and identified the primary influencing factors. The results were as follows. (1) During November and December each year, large flocks of swan geese stopped over at the Yellow River Estuary, primarily distributed in areas surrounding the southern Yellow River channel. (2) Swan goose distribution was jointly influenced by environmental variables at pixel, patch, and landscape scales. The effects of each variable remained stable across months. Slope, distance to water sources, monthly Normalized Difference Vegetation Index (NDVI), mean nearest-neighbor patch distance, road density, and reed wetland proportion exerted strong or moderate negative effects on swan goose distribution. Patch shape index, Simpson diversity index, mudflat area proportion, farmland area proportion, river channel area proportion, and elevation exerted strong or moderate positive effects. (3) The core protected area covered approximately 43% of the swan goose population. Among priority conservation areas accommodating 80% of the population, 23.2—78.2 km² fell within general control zones. These areas consisted primarily of mudflats and reed wetlands on the southern side of the Yellow River channel. It is recommended that strict control of human disturbance should be implemented in key Swan Goose habitats within general control zones during the stopover period, and salinized mudflats and reed wetlands should be restored as a priority during non-stopover period. Moreover, ecological compensation mechanisms should be improved to reduce economic losses for stakeholders associated with aquaculture ponds and farmland.