The fermentation metabolites closely determine the quality of jujube wine, however, little is known about the dynamics of these metabolites during the fermentation process. In this study, a total of 107 volatile and 1758 non-volatile compounds were identified based on flavor-directed research strategy and non-targeted metabolomics. The partial least squares analysis revealed that the major cut-off points for high changes were the 4th and 12th day for the volatile compounds and the 2nd and 10th day for the non-volatile metabolites. After the 10th day of fermentation, the concentration of most volatile compounds decreased by 96%, and the aroma of jujube wine changed from a grass, mushroom, and clay flavor to a floral and fruity flavor. Furthermore, pathway analysis identified four key metabolic pathways and two key metabolic substrates, pyruvate and L-aspartate. This study provides a theoretical reference for optimizing the fermentation process and enhancing the quality of jujube wine.