There is a growing interest in screening α-amylase inhibitors from natural products for application in the development of new antidiabetic drugs or functional foods. In this study, a structure-based virtual screening was applied to rapidly identify the α-amylase inhibitors from medicine food homology (MFH) plants. Similarity search, docking & scoring were used for further filter small molecules. As a result, 21 corresponding potential α-amylase inhibitors from MFH plants were obtained. And, six polyphenol compounds (curcumin, procyanidins, epicatechin gallate (ECG), epigallocatechin gallate (EGCG), hesperidin, and puerarin) were highlighted for further verification after a thorough assessment of the classification of hit molecules as well as docking scores. The results of the enzyme inhibition test showed that ECG, EGCG, and procyanidins had the better binding ability of α-amylase among these six polyphenols. The Ki values of ECG, EGCG, and procyanidins on α-amylase were 0.70, 1.68, and 0.24, respectively. The CD spectra results indicated that the three polyphenols can cause conformational changes in α-amylase.