Lactic acid bacteria (LAB) fermentation can enhance the quality and flavor characteristics of fruit juice. Herein, the impact of individual Lactiplantibacillus plantarum subsp. plantarum (L. plantarum) or Streptococcus thermophilus (S. thermophilus) and co-fermentation of them on jujube juice was compared, and their quality characteristics, volatile and non-volatile compounds were investigated. The results showed that the co-fermentation of selected LAB strains effectively improved the quality of fermented jujube juice (FJJ) as expected, and the types and content of volatile organic compounds (VOCs) increased in FJJs. Among them, the co-fermented sample posed relatively high content of aroma-active compounds with OAV ≥1 (nonanal, decanal, etc), benzaldehyde and acids compared with others, contributing to a more attractive and pleasant flavor. Moreover, non-targeted metabolomic analysis identified 114 and 79 differential metabolites (DMs) between co-fermented and L. plantarum fermented or S. thermophilus fermented samples, respectively. Notably, carboxylic acids and their derivative metabolites as well as organic acids were the crucial components affecting the quality of FJJ. Furthermore, metabolic pathways of DMs of different samples were predominantly enriched in “biosynthesis” and “metabolism”, such as aline, leucine, and isoleucine biosynthesis pathway. Therefore, co-fermentation could enrich the acids, essential amino acid, and VOCs, thereby improving its quality and flavor characteristics. The correlation analysis revealed that most of key VOCs were positively or negatively correlated with D-galacturonate, indicating the importance of D-galactose pathway. Thus, this study provided a theoretical foundation for enhancing the quality and flavor of jujube juice through LAB co-fermentation, offering valuable insights for improving the juice processing.