Some herbal medicines have anti-inflammatory and anti-diarrheal effects. This study analyzed the modulating effect of gut microbiota of anti-inflammatory herbal medicines on antibiotic-associated diarrhea (AAD). The anti-inflammatory effects of 10 herbal medicines and Lizhong-tang active compounds were studied by measuring the nitric oxide production in an in vitro experiment. This was followed by an in vivo experiment in which the anti-diarrheal effects of Lizhong-tang and Magnolia officinalis in a lincomycin-induced AAD mouse model were measured. Changes in the intestinal microflora were observed using terminal restriction fragment length polymorphism analysis. Both Lizhong-tang and M. officinalis were effective against AAD, with Lizhong-tang’s anti-diarrheal effects being particularly effective. In addition, the active compounds of Lizhong-tang, liquiritin and 6-gingerol, inhibited the expression of inducible nitric oxide synthase and cyclooxygenase-2, thus showing an anti-inflammatory effect. Gut microbiota analysis showed that Lizhong-tang could alter the composition of the gut microbiota and ameliorated imbalance in the gut microbiota in a lincomycin-induced AAD mouse model.