The decline of migratory shorebirds in the East Asian-Australasian Flyway has attracted global attention. Conservation efforts thus far have targeted habitat loss and degradation in the Yellow Sea region, with little attention having been given to direct mortality by humans. Here we studied the impacts of direct mortality of shorebirds along China's coast during migration from hunting, fishery bycatch and, at aquaculture sites, bird deterrence measures. We estimated that approximately 47,870 shorebirds were killed at 19 stopover sites per year, mainly from hunting and deterrence. Mortalities for 11 shorebird species account for 1% to 10% of their known total flyway populations. Conservative annual direct mortality rates for four species exceeded sustainable levels, with nine other species approaching unsustainable levels. Direct mortality due to humans is clearly a major overlooked threat to migratory shorebird populations along the East Asian-Australasian Flyway. Reducing it is essential to conserving these declining species.