Tobacco　leaves　need　to　aged　under　certain　temperatures　and　humidity　for　1　to　3　years.　Natural　aging,　also　called　fermentation,　is　a　slow　process.　This　article　explores　the　correlation　between　microorganisms　on　the　surface　of　flue-cured　tobacco　and　key　flavor　substances　during　this　process.　High-throughput　sequencing　was　used　to　characterize　the　composition　of　bacterial　and　fungal　communities　on　the　surface　of　flue-cured　tobacco　from　Hunan,　Liaoning,　Guizhou,　Shandong,　Yunnan,　Fujian,　Brazil,　and　Zimbabwe.　Gas　chromatography—mass　spectrometry　(GC-MS)　was　employed　to　determine　the　flavor　substances　in　flue-cured　tobacco　and　correlation　analysis　between　microbial　diversity　and　flavor　substances　was　performed.　The　function　and　abundance　of　key　enzymes　involved　in　the　degradation　of　macromolecules　on　the　surface　of　flue-cured　tobacco　were　predicted　using　PICRUSt　and　FUNGuild.　Different　flavor　styles　of　flue-cured　tobacco　possessed　different　flora　structures,　and　the　abundance　of　the　genus　Bacillus　was　high　and　significantly　positively　correlated　with　the　content　of　the　main　flavor　substances—carotenoid　and　cembranoid　degradation　products　(p　＜　0.05).　The　content　of　the　Enterobacter　genus　was　higher　in　light-flavor　style　flue-cured　tobacco　and　significantly　negatively　correlated　with　the　above　substances　(p　＜　0.05).　Among　the　fungal　genera,　Wallemia　exhibited　a　significantly　positive　correlation　with　phenylacetic　acid,　palmitic　acid,　and　α-ionol　(p　＜　0.05).　The　abundance　of　the　macromolecule-degrading　enzymes　in　the　bacterial　community　was　generally　higher　than　in　the　fungal　community,　especially　the　enzymes　that　hydrolyzed,　transferred,　and　isomerized　starch,　protein,　and　cellulose.　Classifying　the　tobacco　leaves　according　to　the　flavor　style　revealed　that　the　expression　levels　of　a　series　of　enzymes　acting　on　pectin　hydrolysis　and　cleavage　and　laccase　were　higher　in　strong-flavor　flue-cured　tobacco.　This　study　explored　the　microorganisms　related　to　the　key　substances　of　flue-cured　tobacco　and　provided　a　theoretical　basis　for　using　microorganisms　to　improve　the　flavor.　©　2023　Taylor　&　Francis　Group,　LLC.