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In this study, the effect of microwave-ultrasound or/and toughening treatment on the physicochemical, structural properties, and in vitro digestibility of A- and B-type granules isolated from wheat starch were investigated. From the SEM, microwave-ultrasound and toughening treatment (MU-T) led to the appearance of irregular and disrupted structure significantly and an increment in the resistant starch content of A- and B-type granule. Furthermore, the MU-T starch possessed the lowest swelling power, light transmittance, and gelatinization temperature range (Tc -To) and the highest ΔH. After MU-T, the relative crystallinity (RC) of X-ray pattern, Fourier transform infrared ratio of 1047/1022 cm-1, and the content of double helix and single helix of 13C CP/MAS NMR had increased significantly. In particular, there was a difference in the content of RS and SDS between A-starch granules and B-starch granules as well as their changes after modification (from 69.305% to 82.93 for A-starch and form 74.97% to 88.17 for B-starch, respectively), which was a similar trend with RC and helix content. This study indicated that, for both A-type granule and B-type granule starches, microwave-ultrasound and toughening treated samples had unique properties compared to singly modified starches.