In order to understand the relationship between the aggregation structure and physicochemical characteristics of ultrasonicated sweet potato starches, sweet potato starch modified with different sonication time (15, 20, 25 and 30 min) was studied in this work for developing starch-based ingredients with tailored functionality. SEM, XRD, FTIR, Raman and DSC measurements were conducted to investigate the transformations of morphological features, crystalline structure, short-range ordered structure and ordered molecular structure of starch granules. Not only could pores and cracks be observed at the surface of starch, but also the structural disorganizations were more evidently induced with the treatment time increasing, especially for the degrees of crystallinity, short-range molecular orders and ordered molecular structures. And these disordering in the aggregation structure not only increased the swelling power and solubility but also declined the pasting temperature, peak viscosity, final and breakdown viscosity of gelatinized starch. In addition, the strengthened retrogradation and gel structures formed by the rearrangement and entanglement of starch polymer chains also demonstrated the structural disorganizations of starch granules during ultrasonic treatment. Therefore, the results of this study may provide further insight in understanding the structural basis of starch physicochemical properties.