Background: The Eurasian Spoonbill (Platalea leucorodia) occurs throughout Eurasia and North and sub-Saharan Africa, with three recognized subspecies and six geographically distributed populations. However, in China, we knew almost nothing about migration routes, habitat use and effectiveness of current site protection measures for this species. Methods: We deployed Global Positioning System/Global System for Mobile Communications (GPS/GSM) satellite trackers on 29 Eurasian Spoonbills captured in summer in Mongolia and northeastern China, to obtain complete migration routes data from 10 individuals from 19 complete migration episodes. Results: Tracking data showed no geographical overlap during the annual cycle in Eurasian Spoonbills marked in the two main summering areas. Birds marked in the Naoli River Basin in Heilongjiang Province, China, wintered along the Jiangsu coastline in China, while Eurasian Spoonbills from two discrete summering areas (in Inner and western Mongolia) overwintered inland in the Yangtze River floodplain of China. Excluding the single Inner Mongolian bird, spring migration was significantly faster than autumn migration in the other two groups of birds. Eurasian Spoonbills mainly used water, wetland and grassland habitats in summer, but almost exclusively water in winter. Lack of protection of staging sites used by all the birds in spring and poor levels of protection throughout the annual cycle for western Mongolian birds (5–22%) gives considerable cause for concern, although sites used in other time by East Mongolian and Naoli River birds in the rest of their annual life cycle enjoyed good levels of protection (49–95%). Conclusions: These results revealed previously unknown relationships between summering and wintering areas, migration routes and stopover sites for Eurasian Spoonbills wintering in China, suggesting the existence of discrete biogeographical population units. They also identified winter habitat use of Eurasian Spoonbills in China, confirming open water habitats as being critical throughout the annual cycle, although based on small sample size, gaps in current site safeguard networks for these populations.