Gas chromatography-ion mobility spectrometry (GC-IMS) was used to analyze the characteristics and flavor components of 31 jujube samples from three major production areas around the Tarim Basin in Xinjiang autonomous region, Xinzheng in Henan province and Linxian in Shanxi province. GC-IMS flavor fingerprints were constructed to visually identify the differences in the volatile organic jujubes from different geographical origins. The volatile flavor compounds of Huizao and Junzao jujubes from the regions in Xinjiang were significantly different from those of the jujubes from their native habitats. 1-Octene-3-ol (D), 2-methylpropionic acid, 3-octanone (D), butyric acid, and hydroxyacetone contributed the most to the aroma of Huizao jujube. The volatile organic compounds that contributed the most to the aroma of Junzao jujube were propanal, acetone, 3-methyl butyral, octanal (M), and nonanal (M).