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Exploring the effect of climate changes on population fluctuation of red-crowned crane is of great significance for the species protection and management. Here, based on the annual maximum population size of red-crowned crane wintering in Yancheng Nature Reserve (YNR) from 1981 to 2016, we tested the correlation between population size and the climate variables. The results showed that mean air temperature in wintering period showed a linear upward trend. Annual maximum wintering crane population was 623 +/- 33. Fitting the population size and the climate variables in the same year with GAMs indicated significant correlations between population size and mean maximum air temperature in November, mean minimum air temperature in December, mean air temperature in December, respectively. Time-lag effects were found between population fluctuation of red-crowned crane and the climate variables within 2, 4, 6 and 7 years earlier in December and February of the following year. Combination of the highest interpretations of the climate variables on population size included mean air temperature in January of the following year 6 years earlier, precipitation in January of the following year 7 years earlier and mean air temperature in December. Our results highlighted the importance of considering the effects of long-term climate variables on the population size of endangered birds, red-crowned crane. Then, an interpretation model with high deviance explained was explored. More and continuous attention should be paid to improve considerable measures of crane conservation based on climate change.