The structure and physicochemical properties of starch are important factors to determine the quality of foxtail millet. While hybrid foxtail millet has made greater progress in yield, it has made slower progress in quality than conventional foxtail millet with a more complex genetic base, which was jointly influenced by the parents. However, there were no reports on the comparison of the starch structure and physicochemical properties of hybrid foxtail millets and their parents. In this study, the amylose content, morphology structure, granule size distribution, XRD diffraction, short-range ordered structure, pasting properties, and thermal characteristics of starches derived from Changzagu 466, 333, and 2922 and their parent materials were analyzed. The results showed that compared with male parents, the average particle size, d(0.1), d(0.5), and ΔH of starch from Changzagu 466, 333, and 2922 and their female parents were comparatively larger, while the amylose content values of three hybrid foxtail millets were 26.0%, 28.8%, and 28.9%, which were between the parental (25.8~27.1%, 25.4~28.8%, and 23.6~29.5%), with Tc being higher than the parents and having a lower breakdown viscosity. The peak viscosity of Changzagu 466 and Changzagu 2922 was 5235.5 cP and 5190.8 cP, respectively, lower than that of their parents (5321.0~6006.0 cP and 5257.0~5580.7 cP), while the peak viscosity of Changzagu 333 was 5473.8 cP, falling between the parental values (5337.5~5639.5 cP). The cluster analysis results showed that the starch structure and physicochemical properties of hybrid foxtail millet were significantly different from those of female parents, which were mainly influenced by male parents. The findings of this study will establish a theoretical foundation for the enhancement and innovation of high-quality foxtail millet germplasm resources, as well as the development of high-quality hybrid foxtail millet combinations.