We assessed the effects of wind conditions on stopover decisions and fuel stores of migratory shorebirds at Chongming Dongtan in the south Yellow Sea along the East Asian–Australasian Flyway. In spring and autumn, wind directions differed among altitudes and wind speed generally increased with altitude. Numbers of shorebirds were related to wind effects at low altitudes (on the ground and at 300 and 800 m above the ground), wind effects at 300 m being the best predictor of shorebird numbers. In spring, total number of shorebirds and numbers of the four most abundant shorebird species were negatively related to wind assistance at low altitudes, more birds departing when tailwinds prevailed and more arriving when headwinds prevailed. In autumn, however, total number of shorebirds and numbers of the four most abundant species were positively related to wind assistance at low altitudes, more birds departing and more arriving with tailwinds than with headwinds. When tailwinds prevailed, the number of arriving birds was higher than the number of departing birds. The fuel stores of captured shorebirds, represented by their body mass, was related to wind effects and change in wind conditions between two consecutive days in both spring and autumn, captured birds being heavier when headwinds prevailed than in tailwind conditions, and when the wind conditions became less favourable for flight between two consecutive days. Our results suggest that wind conditions affect stopover decisions and fuel stores, and thus the optimal migration and fuel deposition strategies of migratory shorebirds.