Foxtail millet is a plant that is highly drought-resistant and rich in nutrients. Its grain structure traits are linked with water uptake during grain germination, which is closely related to plant density for high yield under rain fed regions; however, there is no related research. Using Micro-CT technology, we investigated a total of 15 internal structure traits of foxtail millet grains, such as the volume and surface area of the embryo, endosperm, cavity, hull, and whole grain, and mapped relevant quantitative trait loci (QTLs) using recombination inbred lines (RILs). With phenotypic variations in these traits and genome sequences of 100 foxtail millet RILs, four QTLs were identified. In combination with transcriptome profiling during grain development, we identified seven candidate genes that may play a role in the regulation of grain structure in foxtail millet.