An accurate high-performance anion-exchange chromatography (HPAEC) method is presented to measure the inhibition property of flavonoids against mammalian starch digestive enzymes, because flavonoids interfere with commonly used 3,5-dinitrosalicylic acid (DNS) and glucose oxidase/peroxidase (GOPOD) methods. Eriodictyol, luteolin, and quercetin increased absorbance values (without substrate) in the DNS assay and, with substrate, either overestimated or underestimated values in the DNS and GOPOD assays. Using a direct HPAEC measurement method, flavonoids showed different inhibition properties against α-amylase and α-glucosidases, showing different inhibition constants (Ki) and mechanisms. The double bond between C2 and C3 on the C-ring of flavonoids appeared particularly important to inhibit α-amylase, while the hydroxyl group (OH) at C3 of the C-ring was related to inhibition of α-glucosidases. This study shows that direct measurement of starch digestion products by HPAEC should be used in inhibition studies, and provides insights into structure-function aspects of polyphenols in controlling starch digestion rate.