As　a　common　kind　of　food,　pepper　is　well　known　for　its　special　effects　on　the　physiological　state　of　human　individuals.　Capsaicin,　the　main　component　of　pepper,　is　speculated　to　be　linked　with　intestinal　microorganisms　on　account　of　their　direct　contact.　Herein,　we　first　utilized　mouse　models　and　16S　rRNA　high-throughput　sequencing　to　compare　the　differences　in　intestinal　flora　between　mouse　groups　with　and　without　capsaicin　treatment　by　gavage.　The　mice　in　the　two　groups　showed　significantly　distinct　performance　in　terms　of　body　weight,　leukocyte　count,　fecal　humidity,　and　constituent　ratios　of　intestinal　bacteria,　such　as　Faecalibacterium,　Akkermansia,　Roseburia,　Helicobacter,　and　Bacteroides　species.　In　particular,　the　Faecalibacterium　abundance　was　the　most　highly　variable　among　the　5　bacterial　genera.　Based　on　statistical　analysis　and　comparison,　the　variation　tendency　of　body　weight,　leukocyte　count,　and　fecal　humidity　was　closely　related　to　the　bacteria.　In　conclusion,　capsaicin　could　affect　the　physiological　state　of　mice　by　changing　the　constitution　of　the　intestinal　flora.