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Volatile components in jujube fruits from Zizyphus jujuba Mill. cv. Dongzao (DZ) and Zizyphus jujuba Mill. cv. Jinsixiaozao (JS) were analyzed under different cold storage periods via headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). Results identified 53 peaks that corresponded to 47 compounds and were mostly alcohols, aldehydes, esters, and ketones. Differences in the volatile components of jujube fruits were revealed in topographic plots and fingerprints. For DZ, 3-pentanone was the characteristic component of fresh fruits. After storage for 15 days, dipropyl disulfide became the most special substance. Moreover, when stored for 30 and 45 days, the fruits had some same volatile components, like 2-pentyl furan and diallyl sulfide. However, for DZ stored for 60 days, esters were the prominent constituent of the volatile components, simultaneously, some new alcohols appeared. For JS, 2-ethyl furan was the representative of fresh fruits, and 2-butoxyethanol content was the most abundant after 15 and 30 days of storage. Different from that in DZ, the content of ester in JS increased after storage for 45 days. Substances such as amyl acetate dimer, methyl salicylate, and linalool greatly contributed to the jujube flavor during the late storage period. Principal component analysis (PCA) showed that fresh samples and refrigerated fruits were effectively distinguished. Heat map clustering analysis displayed the similarity of volatile components in different samples and was in accordance with PCA results. Hence, the volatile components of jujube fruits can be readily identified via HS-GC-IMS, and jujube fruits can be classified at different periods based on the difference of volatile components.