Black waxy rice wine fermentation metabolites are closely related to the product's final quality. However, little is known about dynamic metabolite changes during fermentation. Here, we used gas chromatography time‐of‐flight mass spectrometry (GC‐TOF‐MS) metabolomics and multivariate statistical analysis to explore the relationship between metabolites and fermentation time. A total of 159 metabolites were identified during the entire fermentation process. The PCA analysis revealed a clear separation between the samples after 4 days and 2 days, and the samples after 4–24 days clustered together. This indicated that BGRW fermentation progresses rapidly in the first 48 hr of fermentation. A total of 40 metabolites were identified as differential during fermentation (VIP > 1 and p < .05), including 12 organic acids, four amino acids, one fatty acid, 17 sugars and sugar alcohols, one alcohol, and five other metabolites. Pathway analysis showed that the differential metabolites were involved in 28 metabolic pathways, and the most commonly influenced pathways (impact value > 0.1 and p < .05) were galactose metabolism, pyruvate metabolism; starch and sucrose metabolism; alanine, aspartic acid, and glutamate metabolism; the tricarboxylic acid cycle, glyoxylic acid, and dicarboxylic acid metabolism; and amino sugar and nucleotide sugar metabolism. Moreover, the integrated metabolic pathway was generated to understand the transformation and accumulation of differential metabolites. Overall, these results provide a comprehensive overview of metabolite changes during black waxy rice wine fermentation.