The gut microbiota， including probiotics and pathogenic microorganisms， is involved in ulcerative colitis (UC) by regulating pathogenic microorganisms and the production of intestinal mucosal antibodies. Huangqin decoction (HQD)， a traditional Chinese formula chronicled in the Shanghan lun， has been recognized as an effective drug for UC， owing to its anti-inflammatory and anti-oxidative properties. In the present study， we investigated whether HQD ameliorates dextran sulphate sodium (DSS)-induced colitis through alteration of the gut microbiota. We found that HQD significantly inhibited colitis， alleviating the loss of body weight， disease activity index， colon shortening， tissue injury， and inflammatory cytokine changes induced by DSS treatment. Principal component analysis and principal co-ordinate analysis showed an obvious difference among the groups， with increased diversity in the DSS and DSS+HQD groups. Linear discriminant analysis effect size was used to determine differences between the groups. The relative abundance of Lactococcus was higher in the DSS+HQD group than in the DSS group， whereas Desulfovibrio and Helicobacter were decreased. Furthermore， the protective effect of HQD was attenuated only in antibiotic-treated mice. In conclusion， our results suggest that HQD could ameliorate DSS-induced inflammation through alteration of the gut microbiota.