In this paper, five Wickerhamomyces anomalus accumulated 9.1–19.7% less released CO2 than S. cerevisiae in the synthetic must. Untargeted metabolomics was used to analyze co-fermented real Cabernet Sauvignon wines. The results showed that all W. anomalus strains significantly decreased the levels of malic acid and hypoxanthine in co-fermented wines, thereby promoting the process of TCA cycle and purine metabolism, respectively. Furthermore, WG5, WG26, and WG27 strains utilized more amino acid, thus favoring the enhancement of aroma compounds. WG27 strain also could biotransform more odorless metabolites into flavor active compounds, such as phenethyl alcohol, indole and indole-3-acetaldehyde. Notably, WG27 strain significantly up-regulated secondary metabolites by more than 400% compared to the other W. anomalus strains. These secondary metabolites were involved in phenylpropanoid and flavonoid metabolism, tryptophan metabolism and methionine metabolism. In addition, co-fermentation with the WG27 strain also resulted in an increase in antioxidant activities by more than 16.09% compared to the control wine. This suggests that the WG27 strain not only improves the flavor and style of the wine but also enhances its antioxidant properties. The findings can be helpful in expanding general understanding of W. anomalus and its potential applications in the food and beverage industry.