Freeze drying can generate high quality food products characterized by good sensory and maximizing the nutritional retention. To mark clear the characteristic compositions of freeze-dried jujubes as affected by varieties, characteristic amino acids, fatty acids, phenolics and their derivatives of 10 varieties of freeze-dried jujube slices were analyzed based on metabolomics. Results showed a total of 55 characteristic amino acids and their derivatives, 34 characteristic fatty acids and their derivatives and 22 characteristic phenolics and their derivatives were identified in 10 varieties of freeze-dried jujube slices. D-Proline (7 146–11 433 mg/100 g), asparagine (1 124–3 609 mg/100 g), suberic (59.41–562.60 mg/100 g), dodecanedioic acid (45.44–304.60 mg/100 g), catechin (6.70–170.10 mg/100 g) and quercetin (11.51–293.90 mg/100 g) were common, and significant (P < 0.05) differences of them were presented in 10 varieties of freeze-dried jujube slices. The differences and characteristic compositions of varieties of freeze-dried jujube slices could be well distinguished by principal component analysis. In conclusion, duing to the highest total content of amino acid, fatty acid, phenolic, respectively GTZ (22 560 mg/100 g), NYDZ (4 106 mg/100 g) and JXSZ (3 582 mg/100 g) were potential varieties for freeze-dried jujube slices. Moreover, the acceptable jujube variety for freeze drying could also be selected based on the characteristic individual composition of amino acid, fatty acid, phenolic and their derivatives, respectively.