S: Hongyingzi is a special waxy sorghum ( Sorghum bicolor L. Moench) cultivar for brewing Moutai liquor. For an overall understanding of the whole genome of Hongyingzi, we performed whole-genome resequencing technology with 56.10 X depth to reveal its comprehensive variations. Compared with the BTx623 reference genome, 2.48% of genome sequences were altered in the Hongyingzi genome. Among these alterations, there were 1885774 single nucleotide polymorphisms (SNPs), 309381 small fragments insertions and deletions (Indels), 31966 structural variations (SVs), and 217273 copy number variations (CNVs). These alterations conferred 29614 genes variations. It was also predicted that 35 genes variations were related to the multidrug and toxic efflux (MATE) transporter, chalcone synthase (CHS), ATPase isoform 10 (AHA10) transporter, dihydroflavonol-4-reductase (DFR), the laccase 15 (LAC15), flavonol 3′-hydroxylase (F3′H), flavanone 3-hydroxylase (F3H), O -methyltransferase (OMT), flavonoid 3′5′ hydroxylase (F3′5′H), UDP-glucose:sterol-glucosyltransferase (SGT), flavonol synthase (FLS), and chalcone isomerase (CHI) involved in the tannin synthesis. These results would provide theoretical supports for the molecular markers developments and gene function studies related to the liquor-making traits, and the genetic improvement of waxy sorghum based on the genome editing technology.