The physical properties of sorghum grains are the key factors affecting liquor-brewing process, and identification of QTL/genes for these traits is of great significance for genetic improvement in liquor sorghum. In this study, the recombinant inbred line population (RIL) consisting of 244 lines from two parental lines ‘654’ and ‘LTR108’ was genotyped using whole-genome resequencing technology, and an ultra-high-density genetic map with 3418 Bin markers was constructed. In 2021 and 2022, the thickness and color of pericarp and testa of 244 RILs were investigated at two locations (Lingshui city and Ledong city, Hainan province, China). Using complete interval mapping (ICIM), a total of 25 QTL for seven traits (exocarp thickness, mesocarp thickness, pericarp thickness, testa thickness, total thickness, exocarp color, and testa color) were identified on chromosomes 1, 2, 3, 4, 5, 8, and 10. An important QTL on chromosome 2 (57.83-57.96 Mb) was repeatedly detected across multiple traits and multiple environments, which is co-localized with the Z locus that controls the mesocarp thickness. Three candidate genes (Sobic.002G204200, Sobic.002G206700 and Sobic.002G206750) were identified and annotated by sequence homology to encode for ubiquitin family proteins and polyamine anabolism-related proteins, and they were reported involving in regulating seed size formation in other crops. This study laid the foundation for Z gene cloning and molecular marker assisted selection technique in liquor sorghum breeding.