Objective To compare the differences in the intestinal microflora of WHBE rabbit and JW rabbit models of diarrhea-predominant irritable bowel syndrome (IBS). Methods 16 WHBE rabbits and 16 JW rabbits were randomly divided into normal control (NC) group and IBS model group, respectively (n = 8). The diarrhea-predominant IBS model was established by wet-heat stress combined with intragastric gavage of senna decoction. The abdominal circumference index, water content of feces and colonic transit function were observed. After sacrifice, colon tissue samples were taken for histopathological examination and colon contents for intestinal flora diversity analysis. Results Compared with the NC group, the IBS model rabbits showed an increased abdominal circumference index and fecal water content, and a shortened colon transit time, but no obvious pathological changes were observed in the colon tissues. Meanwhile, the Shannon index and Chao1 index of IBS model rabbits were significantly decreased ( P <0.05). According to the result of OTU classification analysis, Firmicutes and Bacteroidetes are the dominant bacteria in the intestinal microflora of rabbits. Compared with the NC group, the Firmicutes, Verrucomicrobia, Chloroflexi, Akkermansia, and Streptococcus in the WHBE rabbit IBS model group were significantly reduced ( P < 0.05, P < 0.01), while Bacteroidetes and rc4-4 significantly increased ( P < 0.05, P < 0.01). However, in the JW rabbit IBS model group, Eubacterium and Subdoligranulum were significantly increased ( P < 0.05), while Lactobacillus, Coprobacter, Veillonella and Streptococcus were markedly decreased ( P <0.05). Compared with the JW rabbit NC group, the abundance of Firmicutes, Odoribacter, Veillonella, Streptococcus, Oscillospira and Pseudoflavonifractor were significantly decreased ( P < 0.05, P < 0.01), but Bacteroidetes, Verrucomicrobia, Eubacterium, Akkermansia and Coprobacter were significantly increased ( P <0.05, P <0.01) in the WHBE rabbit NC group. Compared with the JW rabbit IBS model group, the abundance of rc4-4, Bacteroidetes, Coprobacter and Clostridium were significantly higher ( P < 0.05, P < 0.01), while the Firmicutes, Dorea, Coprococcus and Subdoligranulum were significantly lower ( P < 0.05) in the WHBE rabbit IBS model group. Conclusions There is an intestinal microflora imbalance in rabbits with IBS, resulting in a decrease of microflora diversity. The changes of intestinal microflora in the WHBE rabbits and JW rabbits with IBS have their own characteristics, and have apparent differences.