Jiuqu　(starter)　makes　an　important　contribution　to　the　formation　of　the　flavor　characteristics　of　Hongqu　rice　wine　(HQW).　Gutian　Qu　(GTQ)　and　Wuyi　Qu　(WYQ)　are　two　kinds　of　Jiuqu　commonly　used　in　HQW　brewing,　but　the　comparison　of　the　two　kinds　of　HQW　is　still　insufficient　at　present.　The　objective　of　this　study　was　to　compare　the　dynamic　changes　of　amino　acids　(AAs),　higher　alcohols　(HAs),　bioamines　(BAs),　volatile　flavor　compounds　(VFCs),　and　microbial　communities　in　HQW　fermentation,　with　GTQ　and　WYQ　as　starter.　This　study　used　an　automatic　amino　acid　analyzer,　GC,　HPLC,　and　GC-MS　to　detect　AAs,　HAs,　Bas,　and　VFCs　during　fermentation;　metagenomic　sequencing　technology　was　used　to　elucidate　the　microbial　community　and　its　functional　characteristics.　The　results　showed　that　the　contents　of　AAs　and　HAs　in　HQW　brewed　with　WYQ　(WYW)　were　significantly　higher　than　those　in　HQW　brewed　with　GTQ　(GTW).　On　the　contrary,　the　majority　of　BAs　in　GTW　were　significantly　higher　than　those　in　WYW.　The　composition　of　VFCs　in　WYW　and　GTW　were　obviously　different,　as　most　of　the　VFCs　were　notably　enriched　in　WYW,　while　ethyl　caproate,　isoamyl　acetate,　ethyl　heptanoate,　ethyl　nonanoate,　1-decanol,　citronellol,　phenethyl　acetate,　and　hexanoic　acid　were　more　abundant　in　GTW.　Burkholderia　gladioli,　Pantoea　dispersa,　Weissella　cibaria,　Monascus　purpureus,　and　Saccharomyces　cerevisiae　were　the　predominant　microbial　populations　in　GTW　brewing　at　the　species　level,　while　Sphingomonas　sp.,　Kosakonia　cowanii,　Enterobacter　asburiae,　Leuconostoc　lactis,　Aspergillus　niger,　and　Saccharomyces　cerevisiae　were　the　dominant　microbial　species　in　WYW　brewing.　The　abundance　of　functional　genes　involved　in　BAs　biosynthesis　were　much　higher　in　GTW　brewing,　while　the　abundance　of　functional　genes　related　to　the　metabolism　of　characteristic　VFCs　were　much　higher　in　WYW　brewing.　Collectively,　these　findings　provided　evidence　for　elucidating　the　effects　of　Jiuqu　and　microbial　communities　on　HQW　flavor　quality,　and　laid　a　solid　foundation　for　the　improvement　of　HQW　flavor　quality.