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In order to understand the differences of metabolites and their key metabolic pathways between traditional manual and mechanized Huangjiu, gas chromatography-mass spectrometry (GC–MS) combined with non targeted metabolomics was used to track and monitor Huangjiu in the whole post-fermentation stage. The results showed that 25 metabolites and 14 metabolites were identified as differential metabolites in manual and mechanized Huangjiu, respectively (VIP > 1, P < 0.05); three metabolic pathways had significant effects on differential metabolites (−log (P) > 1, impact > 0.01). Compared with the two kinds of Huangjiu, 21 kinds of metabolites were identified as differential metabolites (VIP > 1, P < 0.05); four metabolic pathways had significant effects on differential metabolites (−log (P) > 1, impact > 0.01). This study is helpful to gain insight into the underlying mechanism of flavor formation during the post-fermentation process of Huangjiu and provide a theoretical basis for the industrial development.