Chinese　rice　wine　(CRW)　is　an　alcoholic　beverage　made　mainly　from　rice　or　grain　through　saccharification　and　fermentation　with　Jiuqu　(starter).　Jiuqu　makes　an　important　contribution　to　the　formation　of　the　flavor　characteristics　of　rice　wine.　Hongqu　and　Maiqu　are　two　kinds　of　Jiuqu　commonly　used　in　CRW　brewing.　This　study　compared　the　microbial　community,　biogenic　amines　(BAs),　and　volatile　flavor　components　(VFCs)　of　two　types　of　rice　wine　brewed　with　Hongqu　and　Maiqu　as　fermentation　agents.　The　results　showed　that　the　amino　acid　content　of　rice　wine　fermented　with　Maiqu　(MQW)　was　significantly　lower　than　that　of　rice　wine　fermented　with　Hongqu　(HQW).　On　the　contrary,　the　majority　of　BAs　in　MQW　were　significantly　higher　than　those　in　HQW,　except　for　putrescine.　Multivariate　statistical　analysis　indicated　that　most　of　the　VFCs　detected　were　enriched　in　HQW,　while　ethyl　3-phenylpropanoate　and　citronellol　were　enriched　in　MQW.　The　results　of　metagenomic　analysis　showed　that　Weissiella,　Enterobacter,　Leuconostoc,　Kosakonia,　Saccharomyces,　Aspergilus　and　Monascus　were　identified　as　the　predominant　microbial　genera　in　HQW　brewing　process,　while　Saccharopolyspora,　Lactococcus,　Enterobacter,　Leuconostoc,　Kosakonia,　Pediococcus,　Pantoea,　Saccharomyces,　Aspergillus,　Lichtheimia　and　Nakaseomyces　were　the　predominant　microbial　genera　in　MQW　brewing.　In　addition,　some　VFCs　and　BAs　were　strongly　correlated　with　dominant　microbial　genera　in　HQW　and　MQW　brewing.　Bioinformatics　analysis　showed　that　the　abundance　of　genes　involved　in　BAs　synthesis　in　MQW　brewing　was　much　higher　than　that　in　HQW　brewing,　while　the　abundances　of　genes　related　to　metabolic　pathway　of　characteristic　VFCs　in　HQW　brewing　were　obviously　higher　than　those　in　MQW,　which　explained　the　differences　in　flavor　quality　between　HQW　and　MQW　from　the　perspective　of　microbial　genes.　Collectively,　these　findings　provide　scientific　evidence　for　elucidating　the　contribution　of　different　microbial　genera　to　the　formation　of　flavor　quality　of　CRW,　and　is　helpful　for　screening　beneficial　microbes　to　enhance　flavor　quality　and　drinking　comfort　of　CRW.