The effects of multi-frequencies (mono: 20 kHz, 40 kHz, 60 kHz; dual: 20/40 kHz, 40/60 kHz, 20/60 kHz, and tri: 20/40/60 kHz) on physicochemical properties and in vitro digestibility of arrowhead starch-linoleic acid (AS-LA) complexes were evaluated. The complexing index and FTIR analyses showed that sonication treatment might be helpful in the formation of AS-LA complexes in an ultrasound frequency-dependent manner. The SEM micrographs revealed that the various ultrasonication frequencies caused dense network structure in AS-LA complexes. The XRD showed a V-type crystalline structure with increased crystallinity. Compared with arrowhead starch, a decrease in rapidly digestible starch, and an increase in resistant starch contents of AS-LA under various ultrasound frequencies was due to arrowhead starch and linoleic acid molecular interactions, which inhibited the further binding abilities. As a non-thermal technology, ultrasound could be effectively employed to prepare starch-lipid complexes with significant potential in functional foods and drug delivery systems.