To understand the flavor and metabolite differences between the three commercial dried jujube cultivars Huizao (HZ), Hamazao 1 (HMZ), and Qiyuexian (QYX), their soluble sugars, organic acids, volatiles, and metabolites were systematically investigated. The results show that sucrose and malic acid were the main soluble sugar and organic acids contained in these dried jujubes, respectively. Sucrose (573.89 mg/g DW) had the highest presence in HZ, and the total sugar content (898.33 mg/g DW) was the highest in QYX. Both of these had a low total acid content, resulting in relatively high sugar–acid ratios (105.49 and 127.86, respectively) compared to that of HMZ (51.50). Additionally, 66 volatile components were detected in the 3 jujubes. These mainly included acids, aldehydes, esters, and ketones (90.5–96.49%). Among them, (E)-2-nonenal, (E)-2-decenal, heptanal, decanal, nonanal, and octanal were identified as the key aromatic substances of the dried jujubes, and their contents were the highest in HMZ. Moreover, 454 metabolites were identified, including alkaloids, amino acids, flavonoids, lipids, nucleotides, and terpenoids. The highest contents of flavonoids (5.6%) and lipids (24.9%) were detected in HMZ, the highest contents of nucleotides (10.2%) and alkaloids (27%) were found in QYX, and the contents of saccharides (5.7%) and amino acids (23.6%) were high in HZ. Overall, HZ, HMZ, and QYX significantly differ in their flavor and nutrition. HZ tastes better, HMZ is more fragrant, and QYX and HMZ possess higher nutritional values.