•High pressure decreased the angle of α-1,4 glycosidic linkage.•High pressure increased the dihedral angles of α-1,4 glycosidic linkage.•High pressure made amylose helix be more ‘stout’.•High pressure made amylose polymers be more stable.•High pressure decreased intramolecular H-bonds and increased solvent-amylose H-bonds. For more effective using of HHP (high hydrostatic pressure) in starch processing, in this study, molecular dynamics simulation was used to explore the effects of pressure on amylose molecular conformation at the atomic level. The results shown that, firstly, high pressure decreased the intramolecular hydrogen bonds and increased the amylose-solvent hydrogen bonds, which is consistent with the process of high pressure starch gelatinization. Secondly, high pressure made amylose polymers more “stout”. Meanwhile, high pressure decreased the angle of α-1,4 glycosidic linkage and increased the dihedral angles of α-1,4 glycosidic linkage, which indicates that pressure has obvious effects on amylose molecular conformation. Thirdly, high pressure made amylose polymers more stable. Moreover, in view of the results of energies, HHP may have an opposite gelatinization mechanism to heating. The results may be complementary to the existing experimental phenomena and provide theoretical guidance value for the using of HHP in starch processing.