To overcome the fruit’s perishability, mulberry wine has been developed as a method of preservation. However, dynamic changes in metabolites during mulberry wine fermentation have not been reported yet. In the present investigation, UHPLC-QE-MS/MS coupled with multivariate statistical analyses was employed to scrutinize the metabolic profiles, particularly the flavonoid profiles, throughout the process of vinification. In general, the major differential metabolites encompassed organic heterocyclic compounds, amino acids, phenylpropanoids, aromatic compounds, and carbohydrates. The contents of total sugar and alcohol play a primary role that drove the composition of amino acids, polyphenol, aromatic compound, and organic acid metabolites based on the Mantel test. Importantly, among the flavonoids, abundant in mulberry fruit, luteolin, luteolin-7-O-glucoside, (−)-epiafzelechin, eriodictyol, kaempferol, and quercetin were identified as the differential metabolic markers during blackberry wine fermentation and ripening. Flavonoid, flavone and flavonol biosynthesis were also identified to be the major metabolic pathways of flavonoids in 96 metabolic pathways. These results will provide new information on the dynamic changes in flavonoid profiles during black mulberry winemaking.