Based on the meteorological data from 54 stations in Xinjiang during the period from 1963 to 2012, the values of the standardized precipitation and evapotranspiration index (SPEI) at 12-month timescale were calculated. Meanwhile, the spatiotemporal variation of drought in recent 50 years was analyzed using the methods of linear regression,empirical mode decomposition (EMD) and empirical orthogonal function (EOF). The results showed that the drought condition in Xinjiang in the past 50 years was changed significantly. A drying-to-wetting climate change occurred in Xinjiang since 1987. However, the decreased SPEI12 revealed that an obvious drying trend occurred in Xinjiang in the past decade. Temporally, there were three kinds of variation periods of drought including 2-year period,6-year period and 24-year period. The first mode of EOF explained the consistent pattern of drought in whole Xinjiang,and the second mode of EOF reflected the wetting (or drying) pattern in south Xinjiang and drying(or wetting) pattern in north Xinjiang. The spatiotemporal variation of drought was overall consistency in whole Xinjiang but also heterogeneity at local scale.