Foxtail millet (Setaria italica) is a major cereal crop cultivated in the arid and semi-arid regions of northern China. However, achieving uniform emergence poses a significant challenge in foxtail millet cultivation, despite its remarkable drought resistance. Seed imbibition is an essential germination process influenced by the water uptake capacity, directly affecting the subsequent emergence. This study investigated the water absorption capacity of 300 foxtail millet germplasm resources and identified two candidate genes (Si4g02810 and Si4g02840) associated with saturated water absorption through Genome-wide Association Study (GWAS). The gene's function is hypothesized to be associated with starch synthesis. Haplotype analysis revealed the presence of multiple haplotypes on these genes in upstream, 5 ' UTR, CDS, 3 ' UTR and downstream regions. Moreover, we analyzed the extreme varieties of seed starch content and starch granule characteristics to gain insights into water uptake. Scanning electron microscopy demonstrated that high water uptake varieties exhibited loosely structured starch granules, whereas low water uptake varieties displayed compact starch granules. Our hypothesis is that the compactness of starch granules in seeds may be associated with seed imbibition.