To elucidate starch structural features underlying resistant starch formation, wheat starch granules with three (A-, B- and C- type) crystalline polymorphisms and a range of amylose contents were digested in vitro. The changes in multi-level structure of digestion residues were compared. In the residues of A- and C-type starches, the molecular fine structure (distributions of chain length and whole molecular size), as analyzed by size exclusion chromatography (SEC), remained similar during digestion. In contrast, B-type high amylose wheat starch (HAWS) showed distinct changes in multi-level structures of digestion-resistant fractions: (1) the peak of longer amylopectin branches shifted to a lower degree of polymerization (40 DP); (2) production of α-limit dextrin (~2 nm hydrodynamic radius) in the residues; (3) a small increase of double helix content during digestion, in contrast to 6 % reduction for the A-type starch; (4) a decrease (6 °C lower) in the melting temperature of amylose-lipid complexes. The comparison suggests that elongated branches in B-type starch contribute to the formation of resistant fraction (including α-limit dextrin) against α-amylase. The amorphous packing of starch polymers with elongated branches together with the absence of surface pores and channels is proposed to be the basis for the enzymatic resistance of granular HAWS.