The alpha‐glucosidase inhibitor is a common oral anti‐diabetic drug used for controlling carbohydrates normally converted into simple sugars and absorbed by the intestines. However, some adverse clinical effects have been observed. The present study seeks an alternative drug that can regulate the hyperglycemia by down‐regulating alpha‐glucosidase and alpha‐amylase activity by molecular docking approach to screen the hyperglycemia antagonist against alpha‐glucosidase and alpha‐amylase activities from the 47 natural compounds. The docking data showed that Curcumin, 16‐hydroxy‐cleroda‐3,13‐dine‐16,15‐olide (16‐H), Docosanol, Tetracosanol, Antroquinonol, Berberine, Catechin, Quercetin, Actinodaphnine, and Rutin from 47 natural compounds had binding ability towards alpha‐amylase and alpha‐glucosidase as well. Curcumin had a better biding ability of alpha‐amylase than the other natural compounds. Analyzed alpha‐glucosidase activity reveals natural compound inhibitors (below 0.5 mM) are Curcumin, Actinodaphnine, 16‐H, Quercetin, Berberine, and Catechin when compared to the commercial drug Acarbose (3 mM). A natural compound with alpha‐amylase inhibitors (below 0.5 mM) includes Curcumin, Berberine, Docosanol, 16‐H, Actinodaphnine/Tetracosanol, Catechin, and Quercetin when compared to Acarbose (1 mM). When taken together, the implication is that molecular docking is a fast and effective way to screen alpha‐glucosidase and alpha‐amylase inhibitors as lead compounds of natural sources isolated from medicinal plants. © 2015 BioFactors, 41(4):242–251, 2015