The current research investigated the multi-scale structural interactions between arrowhead starch (AS) and phenolic acids, such as ferulic acid (FA) and gallic acid (GA) to identify the mechanism of anti-digestion effects of starch. AS suspensions containing 10 % (w/w) GA or FA were subjected to physical mixing (PM) followed by heat treatment at 70 °C for 20 min (HT) and a synergistic heat-ultrasound treatment (HUT) for 20 min using a dual-frequency 20/40 KHz system. The synergistic HUT significantly (p < 0.05) increased the dispersion of phenolic acids in the amylose cavity, with GA showing a higher complexation index than FA. XRD analysis showed a typical V-type pattern for GA, indicating the formation of an inclusion complex, while peak intensities decreased for FA following HT and HUT. FTIR revealed sharper peaks possibly of amide bands in the ASGA-HUT sample compared to that of ASFA-HUT. Additionally, the emergence of cracks, fissures, and ruptures was more pronounced in the HUT-treated GA and FA complexes. Raman spectroscopy provided further insight into the structural attributes and compositional changes within the sample matrix. The synergistic application of HUT led to increased particle size in the form of complex aggregates, ultimately improving the digestion resistance of the starch-phenolic acid complexes.