The metabolite changes in adzuki bean, as functional food, and their effects on its biological activity were monitored. The in adzuki bean cultivars were successfully distinguished by multivariate statistical analysis in electrospray ionization mode. As shown by the PCA scatter plot, volcano plot and box plot, the -glucosidase exhibited significant chemical markers derived from 355.1271, 342.1189, 666.2219, and 1133.5381 m/z, whereas the hDPP-IV exhibited tentative chemical markers derived from 666.2220 and 342.1193 m/z. The adzuki bean extracts also inhibited -glucosidase and hDPP-IV differently depending on the secondary metabolites composition. In detail, Milyang59, Haeoreum, Hongda, and Hongyeon inhibited α-glucosidase by 29.3, 16.6, 139.9, and 20.6% at 600 μg/mL, respectively, while Milyang59, Joongwon, Haeoreum and Hongmiin inhibited hDPP-IV by 15.0, 21.0, 15.0, and 20.0% at 600 μg/mL, respectively. Importantly, discrimination was shown across the cultivars of the adzuki bean, which correlated strongly with the azukisaponin VI and their derivatives in Milyang59 and Haeoreum.