Structures and functionality of two groups of high-amylose maize hybrids starches (HAMHSs) with the same maternal parent but different paternal parent were investigated. H1 and H2 (Group 1) and H3 and H4 (Group 2) had the same maternal parents within the groups, respectively. Paternal parent affected the molecular size of amylopectin components of HAMHS as deduced by gel-permeation chromatography (GPC) analysis of native samples. GPC analysis of debranched samples and further amylose fitting analysis showed the paternal parent effect on the average chain lengths of amylose and long amylopectin (DP > 36). WAXS and SAXS data showed paternal parent only affected the thickness of crystalline lamellae and the amorphous lamellae, but had no effect on polymorph type, crystallinity, lamellar ordering, and long periodic distance of HAMHS. In addition, water solubility and contents of rapidly digestible starch, slowly digestible starch, and resistant starch were all affected by the paternal parent. In summary, we report some significant differences of HAMHS with the same maternal parent but different paternal parent.