An accurate hydrophilic interaction liquid chromatography coupled mass spectrometry (HILIC-MS) method is presented to characterize starch digestion by α-amylase and measure the inhibition properties of flavonoids against α-amylase in vitro. Eleven products were found as 1 → 4 linkage glucose oligosaccharides with different degrees of polymerization (DPs) from 2 to 12. The products with DPs of 2, 3, 6, 7, and 9 had higher yields. The product with DP of 9 had the highest yields, which first increased and then decreased with the reaction time. Pelargonidin has the best inhibition activity on all enzyme products. The 3′-hydroxyl of B-ring enhanced the inhibition activity of flavonol and flavone but weakened that of anthocyanin. The C-ring 3-hydroxyl increased the inhibition effect of flavonol on maltose but decreased that on the products with higher DPs than flavone. The HILIC-MS method can provide more detailed information on enzyme products for the study of flavonoids inhibiting α-amylase.