To study the quality discrepancy of jujube vinegar brewed from different jujube varieties, six types of jujube vinegar made from different varieties of jujube were evaluated by the analysis of basic physicochemical components (such as pH, total acid, total phenol and total flavone), color, in vitro functional activity (antioxidant capacity and lipid-lowering ability), organic acids, amino acids, and volatile aroma components, combined with electronic nose and sensory evaluation. The results showed that there were significant differences in the quality of jujube vinegar brewed from different jujubes. In terms of physical and chemical analysis, the total acid and total flavonoids of Xinjiang jujube vinegar were the highest, which were 54.87 g/L and 1168.84 mg RE/L, respectively. By contrast, the total phenolic content of Xinjiang Jun-jujube jujube vinegar was the highest, which was 1815.63 mg GAE/L. Henan Lingbao jujube vinegar and Fuping jujube vinegar had better color values. Xinjiang Jujube vinegar showed the best antioxidant and lipid lowering activities. Fuping jujube vinegar had the lowest total organic acid content of 47.07 g/L. Xinjiang gray jujube vinegar and Xinjiang Jun-jujube vinegar had higher essential amino acid and total amino acid content, while Hebei Fuping jujube vinegar had lower amino acid content. A total of 41 volatile aromas were detected in 6 kinds of jujube vinegar, and there were certain differences in the types and contents of volatile aromas contained in different kinds of jujube vinegar. The sensory evaluation showed that all jujubes were suitable for brewing jujube vinegar, among which Xinjiang Hui-jujube vinegar had the best sensory acceptance. In summary, there were certain differences in the quality of 6 kinds of jujube vinegar. The high functional activity of Xinjiang Jun-jujube vinegar made it more suitable as a functional fruit vinegar. Based on the high sensory acceptance of Xinjiang Hui-jujube vinegar, the Xinjiang Hui-jujube would be suitable for the vinegar processing too.