The molecular and lamellar structures and in vitro digestibility of high amylose maize starch granules were investigated. Size-exclusion chromatography (SEC) analysis of hydrodynamic radius (R-h) and relative contents (RC) of different amylose and amylopectin pools revealed that increased amylose content resulted in the decrease of RC of short amylopectin chains (AP1, DP <36), and the increase of R-h and RC of long amylopectin chains (AP2, DP > 36). Fluorophore-assisted carbohydrate electrophoresis (FACE) analysis showed the average chain lengths of defined structures of fa, fb(1), and fb(3), and the content of fb(3) were increased with the amylose content and at AC content of 43%, the chain lengths decreased with the amylose content. The relative contents of fa and fb(1) and the degree of branching had the converse trends. Hence, HA-2, having an AC content of 43%, was the tipping point for these structural changes. Small angle X-ray scattering (SAXS) and its normalized 1D correlation function and SAXS scattering curve parametric fitting showed that the crystalline lamellar thickness was negatively correlated with proportion of short amylose chains (AM1, 100