JUNCAO wine fermentation metabolites are closely related to the final quality of the product. Currently, there are no studies of dynamic metabolite changes during fermentation of JUNCAO wine. Here, we used gas chromatography quadrupole time-of-flight mass spectrometry (GC-QTOF-MS) metabolomics and multivariate statistical analysis to explore the relationship between metabolites and fermentation time. A total of 189 metabolites were annotated throughout the fermentation process. The principal component analysis (PCA) revealed a clear separation between the samples in the early and late stages of fermentation. A total of 60 metabolites were annotated as differential during the fermentation (variable importance in the projection, VIP > 1, andp< 0.05), including 21 organic acids, 10 amino acids, 15 sugars and sugar alcohols, and 14 other metabolites. Pathway analysis showed that the most commonly influenced pathways (impact value > 0.1 andp< 0.05) were tricarboxylic acid cycle, alanine, aspartic acid and glutamic acid metabolism, pyrimidine metabolism, and other 10 metabolic pathways. Moreover, integrated metabolic pathways are generated to understand the conversion and accumulation of differential metabolites. Overall, these results provide a comprehensive overview of metabolite changes during fermentation of JUNCAO wine.