Amylopectin (AP)-only (APBS), normal (NBS), and amylose (AM) only (AOBS) barley starches were selected here to investigate catalysis pattern of maltogenic α-amylase (MA) on hydrolyzing AP and AM granular starches. MA shortened starch side chains with degree of polymerization (DP) 11–30. MA-treated APBS exhibited porous granular structures and dramatically increased degree of branching (DB, 17–20 %), and reduced ordered degrees, suggesting high hydrolysis and transglycosylation activities of MA. MA-treated NBS showed less pronounced porous structures and slightly increased DB (2–4 %), indicating high hydrolysis but low transglycosylation activities. AOBS displayed minimal changes in DB (0.2–0.3 %) and starch structures, implying low hydrolysis and transglycosylation activities. Therefore, MA preferred to attack the AP molecules with abundant glucan substrates with DP 11–30, while AM restricted MA activity likely by creating ineffective binding sites and undergoing rapid reorganization. These findings deepened the understanding of the mechanisms of MA in modifying granular starches with varying AM content.