Retarding the starch digestion rate is the key to produce low glycemic index (GI) foods for diabetic patients in prevention of postprandial hyperglycemia. In the search for naturally-occurring starch hydrolase inhibitors as active ingredients for low GI foods, we applied a high throughput assay to screen hundreds of edible botanical materials and discovered that a phenylpropanoid sucrose ester, diboside A (1,3,6′-tri-p-coumaroyl-6-feruloyl sucrose), isolated from the root of wild buckwheat exhibited potent α-amylase inhibitory activity with an IC50 of 26.9μM. Kinetic study revealed that it is an uncompetitive inhibitor of α-amylase with a Ki of 5.1μM. Moreover, diboside A inhibits rat intestinal sucrase as a noncompetitive inhibitor with a Ki of 72.4μM. Remarkably, it has no measurable activity towards maltase. An in silico molecular docking study shows that there are two possible allosteric binding sites between diboside A and enzyme–substrate complex. Binding site one is a more probable binding site because of lower energy of the ternary complex formed by hydrogen bonds and electrostatic interactions. Our results suggest that phenylpropanoid sucrose esters have potential as an active ingredient for low GI foods.