Diabetes is a major chronic disease that jeopardises human health. Resistant starch (RS) is important in controlling diabetes. However, the specific relationship between the starch crystalline structure and RS content needs to be further elucidated. In this study, the details of the interactions between different starch molecules (single-amylose and double-helix) and α-amylase were analysed using molecular docking and dynamic simulations. Single-amylose molecules could penetrate deep into the active groove of α-amylase and make full contact with the catalytic triad, and their G3 and G4 glucose residues were firmly bound to the bottom of the active groove throughout the simulation. However, the double-helix molecule in the crystalline region of starch could not fully penetrate to the bottom of the active groove and make full contact with the catalytic triad of α-amylase. This suggests that, without considering other structural factors, the RS content should be positively correlated with relative crystallinity. In addition, starch molecules had strong interactions with α-amylase (approximately 78 kJ/mol) and could form many hydrogen bonds with the amino acid residues of α-amylase such as Thr163, Gln63, and Ile148, which supports the sliding continuum hydrolysis hypothesis of α-amylase. These results explain the intrinsic relationship between the starch hydrolysis efficiency and crystalline structure at the molecular level and provide an important reference for the preparation of RS and elucidation of its mechanism. •The single-chain starch molecule could penetrate deep into the active groove of α-amylase.•The double-helix molecule could not make full contact with the catalytic triad of α-amylase.•Starch molecules could form many hydrogen bonds of α-amylase.•The RS content should be positively correlated with relative crystallinity.•The results supports the sliding continuum hydrolysis hypothesis of α-amylase.