Rice　wine　is　primarily　crafted　from　grains　through　saccharification　and　liquification　with　the　help　of　Qu.　Qu　plays　an　important　role　in　the　formation　of　the　flavor　quality　of　rice　wine.　Hongqu　and　Xiaoqu　represent　two　prevalent　varieties　of　Qu　that　are　typically　utilized　in　the　brewing　process　of　rice　wine　and　play　a　crucial　role　in　its　production.　In　this　study,　GC,　GC-MS,　HPLC,　and　metagenomic　sequencing　techniques　were　used　to　contrast　the　microbial　flora,　biogenic　amines,　and　aroma　characteristics　developed　during　the　fermentation　of　rice　wines,　with　Hongqu　and　Xiaoqu　being　used　as　initiating　agents　for　the　brewing　process.　The　results　show　that　the　content　of　higher　alcohols　(including　n-propanol,　isobutanol,　3-methyl-1-butanol,　and　phenethyl　alcohol)　in　rice　wine　brewed　with　Xiaoqu　(XQW)　was　significantly　higher　than　that　in　rice　wine　brewed　with　Hongqu　(HQW).　Contrarily,　the　concentration　of　biogenic　amines　in　HQW　surpassed　that　of　XQW　by　a　notable　margin,　but　tyramine　was　significantly　enriched　in　XQW　and　not　detected　in　HQW.　In　addition,　a　multivariate　statistical　analysis　revealed　distinct　disparities　in　the　constitution　of　volatile　components　between　HQW　and　XQW.　Hexanoic　acid,　ethyl　acetate,　isoamyl　acetate,　ethyl　caproate,　ethyl　decanoate,　2-methoxy-4-vinylphenol,　etc.,　were　identified　as　the　characteristic　aroma-active　compounds　in　HQW　and　XQW.　A　microbiome　analysis　based　on　metagenomic　sequencing　showed　that　HQW　and　XQW　had　different　dominant　microorganisms　in　the　brewing　process.　Burkholderia,　Klebsiella,　Leuconostoc,　Monascus,　and　Aspergillus　were　identified　as　the　primary　microbial　genera　in　the　HQW　fermentation　period,　while　Pediococcus,　Enterobacter,　Rhizopus,　Ascoidea,　and　Wickerhamomyces　were　the　main　microbial　genera　in　the　XQW　brewing　process.　A　bioinformatics　analysis　revealed　that　the　concentrations　of　microbial　genes　involved　in　biogenic　amines　and　esters　biosynthesis　were　significantly　higher　in　HQW　than　those　in　XQW,　while　the　content　of　genes　relevant　to　glycolysis,　higher　alcohol　biosynthesis,　and　fatty　acid　metabolism　was　significantly　higher　in　XQW　than　in　HQW,　which　are　the　possible　reasons　for　the　difference　in　flavor　quality　between　the　two　kinds　of　rice　wine　from　the　perspective　of　microbial　functional　genes.