Microwave treatment is an environmentally friendly method for modification of high-amylose maize starch (HAMS). Here, the effects of short-time (≤120 s) microwave treatment on the structure and pasting of two types of HAMSs, Gelose 50 (HAMSI) and Gelose 80 (HAMSII), with apparent amylose content (AAC) of 45 % and 58 %, respectively, was studied using a multiscale approach including X-ray scattering, surface structures, particle size distribution, molecular size distributions and high temperature/pressure Rapid Visco Analysis (RVA)-4800 pasting. As compared to starch with no amylose (waxy maize starch, WMS) and 25 % amylose content (normal maize starch, NMS), HAMSI underwent similar structural and pasting changes as WMS and NMS upon microwave treatment, and it might primarily be attributed to the amylopectin fraction that was affected by cleavage of the connector chains between double helices and backbone chains, which decreased the crystallinity and thickness of the crystalline lamellae. However, the multi-scale structure of HAMSII was almost unaffected by this treatment. The pasting properties of fully gelatinized HAMSI starch showed a decrease in RVA-4800 peak and final viscosities after microwave treatment. In contrast, for HAMSII starch, the microwave treatment led to an increase in these viscosities. The combined results highlight the influence of varying AAC on the effects of microwave-mediated modification, leading to diverse alterations in the structure and functionality of starches.