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Huangjiu is a popular Chinese traditional alcoholic beverage, while its brewing processes have rarely been explored. We herein report the first gapless, near-finished genome assembly of the industrial strain Aspergillus flavus SU-16 for huangjiu brewing. This work provides insights and supports for the further industrial applications of A. flavus isolates by comprehensively studying of the safety and genomic variations of SU-16. We demonstrated that SU-16 is a non-aflatoxigenic A. flavus at both molecular and metabolic levels. Using of nanopore sequencing technology resulted in a complete genome sequence for all 8 A. flavus chromosomes, as well as the mitochondrion. Genome comparisons of SU-16 with reference strains identified the chromosomal rearrangements, revealed the adaption mechanism of SU-16 to huangjiu ecological niche, and found that SU-16 is a good repository for CAZymes and some bioactive secondary metabolites. The results will help to develop more scientific huangjiu fermentation processes, and explore metabolism pathways of desired or harmful components in huangjiu to improve its quality. • SU-16 was identified as a non-aflatoxigenic A. flavus strain; • Nanopore sequence technology resulted a gapless, near-finished genome assembly of A. flavus SU16; • Metabolic alterations caused by the accumulation of genetic variations are the main driving force for the functional differentiation of A. flavus during domestication; • SU-16 possesses an incomplete aflatoxin biosynthesis gene cluster; • Results provide insights and supports for the further application of SU-16 in the other fields. [ABSTRACT FROM AUTHOR]