Metabolite profiling of the roasted coffee beans fermented by wild and caged civets (luwak) was assessed by 1 H NMR-based metabolomics. Our result indicated that the metabolite profile of the roasted civet coffee beans possessed uniqueness and was distinct from the regular coffee. According to OPLSDA data, the roasted civet coffee beans contained higher levels of acetic acid, lipid, trigonelline, quinic acid, citric acid, and malic acid than those of regular coffee. The most discriminant metabolites in the caged civet coffee were lipid and acetic acid. Meanwhile, malic acid and citric acid were the distinguishing metabolites in the roasted beans of wild civet coffee. Furthermore, the antioxidant properties and alpha-glucosidase inhibitory activity of the coffee samples were evaluated. The biological activities of the civet coffee beans were better than that of regular coffee. According to the PLS analysis, malic acid was the highest positive correlated with the antioxidant activity and alpha-glucosidase inhibition of the coffee sample. The possibility of coffee fermentation in the civet digestive tract increases malic acid levels so that it has a beneficial effect on its alpha-glucosidase inhibitory activity.