From June 2011 to August 2011 and from June 2012 to August 2012, the nest site selection and the brood habitat selection of Whooper Swans (Cygnus cygnus), which located in Bayanbulak Nature Reserve of Xinjiang, were researched. 26 Whooper swans' nest sites were found in the wild. Compared the found nest sites with the control plots of nest sites, there were significant differences in the factors of vegetation height, water depth, water area, distance to disturbance and security level. What's more, the logistic regression analysis showed that the vegetation height, water depth and the security level were the three most important factors of the nest site selection of Whooper Swans. On the analysis of brood habitat selection, it was found that the Whooper Swans selected the swamp and avoided the grass land. Compared the found brood habitat with the control plots of brood habitat, there ware significant differences in nine factors, and the logistic regression analysis showed that the distance to disturbance and the security level were the important factors determinating the brood habitat selection of Whooper Swans. The selection mechanisms conducive to Whooper Swans of avoiding predators, and they can complete incubation and brooding successfully.