Abstract: This study was designed to compare intestinal bacteria and inflammatory cytokine expression in rats with ulcerative colitis (UC) after treatment of three regiments, Huang-qin-tang (HQT), Si-shen-wan (SSW), and Tong-xie-yao-fang (TXYF). After approved by Institute of Chinese Materia Medica Ethics Committees in China Academy of Chinese Medical Sciences, UC in rats was induced by using a compound method (trinitrobenzenesulfonic acid plus ethanol). Rats were randomly divided into control, disease, positive control salazosulfapyridine (SASP, 0.5 g·kg^-1), HQT (20 g·kg^-1), SSW (26 g·kg^-1), and TXYF groups (22 g·kg^-1). After 7 days of treatment, colonic tissues and the blood were taken for various assays. Damage of colonic tissues was detected by H&E staining. The levels of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-8 (IL-8) and prostaglandin E₂ (PGE₂) in the serum were detected by the enzyme linked immunosorbent assay (ELISA). Total DNA was extracted from stool samples for analyses of 16SMiseqPE300V3-4 segment using high-throughput sequencing. The inflammatory cytokine results showed that compared with the disease group, the content of IL-6, PGE₂, TNF-α in SASP group were decreased (P<0.05), with the most significant decrease being the level of IL-8 (P<0.01), whereas the levels of IL-6, IL-8 and TNF-α in HQT group were reduced (P<0.05) and PGE₂ content was clearly reduced (P<0.01). The contents of four cytokines in SSW group were decreased, but there was no statistical difference. While the levels of IL-6 and TNF-α in TXYF group were reduced, and the reductions of IL-8 and PGE₂ were significant (P<0.05). The results after sequencing showed that microbiome species richness SSW group > HQT group > TXYF group; the similarity between samples TXYF group > SSW group > HQT group; the species of HQT and TXYF group have greater difference when compared to the disease group. The content of beneficial bacteria in the intestine of HQT group > SSW group > TXYF group. Three regiments all have therapeutic effects on UC, manifested by improvements of the signs and mental status of UC rats. However, in terms of inhibition of inflammatory factors IL-6, IL-8, PGE₂ and TNF-α, and regulation of intestinal microbiome, the therapeutic effect of HQT was superior than SSW and TXYF.