Inhibitors of αâamylase have been developed to regulate postprandial blood glucose fluctuation. The enzyme inhibition arises from direct or indirect inhibitorâenzyme interactions, depending on inhibitor structures. However, an ignored factor, substrate, may also influence or even decide the enzyme inhibition. In this work, it is innovatively found that the difference in substrate enzymolysis modes, i.e., structural composition and concentration of αâ1,4âglucosidic bonds, triggers the diversity in inhibitorâenzyme aggregating behaviors and αâamylase inhibition. For competitive inhibition, there exists an equilibrium between αâamylaseâsubstrate catalytic affinity and inhibitorâαâamylase binding affinity; therefore, a higher enzymolysis affinity and concentration of αâ1,4âglucosidic structures interferes the balance, unfavoring inhibitorâenzyme aggregate formation and thus weakening αâamylase inhibition. For uncompetitive inhibition, the presence of macromolecular starch is necessary instead of micromolecular GalG2CNP, which not only binds with active site but with an assistant flexible loop (involving Gly304âGly309) near the site. Hence, the refined enzyme structure due to the molecular flexibility more likely favors the inhibitor binding with the nonâactive loop, forming an inhibitorâenzymeâstarch ternary aggregate. Conclusively, this study provides a novel insight into the evaluation of αâamylase inhibition regarding the participating role of substrate in inhibitorâenzyme aggregating interactions, emphasizing the selection of appropriate substrates in the development and screening of αâamylase inhibitors.