High-amylose starches are attracting considerable attention because of their potential health benefits and industrial uses. Enzyme hydrolysis of starch is involved in many biological and industrial processes. In this paper, starches were isolated from high-amylose transgenic rice (TRS) and its wild type rice, Te-qing (TQ). The morphological and structural changes of starch residues following Aspergillus niger amyloglucosidase (AAG) hydrolysis were investigated. AAG hydrolysed TQ starch from the granule surface, and TRS starch from the granule interior. During AAG hydrolysis, the content of amorphous structure increased, the contents of ordered structure and single helix decreased, and gelatinisation enthalpy decreased in TQ and TRS starch residues. The A-type polymorph of TRS C-type starch was hydrolysed faster than the B-type polymorph. The short-range ordered structure and B-type polymorph in the peripheral region of the subgranule and the surrounding band of TRS starch increased the resistance of TRS starch to AAG hydrolysis.