Finding ways to sustainably balance human needs with biodiversity conservation is increasingly challenging, especially on densely populated coasts. In China, rising demands for seafood and land intensify pressures on coastal habitats-the most critical refueling sites for migratory shorebirds along the East Asian-Australasian Flyway. Here we report on a continent-wide scale, decade-long field investigation on how China’s extensive intertidal mariculture impacts these vulnerable shorebirds. We show that commercial molluscs have become an essential resource for the molluscivorous shorebirds, determining their large-scale spatial distribution and temporal population dynamics during northward migration. We also reveal the unintended declines in both molluscs and shorebirds following a conservation-motivated mariculture ban, highlighting the “tragedy of the commons” as a consequence of unregulated public use. This study unveils the pivotal yet unforeseen role of China’s intertidal mariculture in sustaining shorebirds along the world’s most threatened flyway. If this delicate balance is disrupted without viable alternative food resources for the shorebirds, a considerable part of the flyway populations will be at risk. Evidence-based policymaking and management are required to harmonize seafood production with biodiversity conservation.