Butyrate-producing bacteria generate butyrate, which has antidepressant effects. Xiaoyaosan (XYS), a traditional Chinese medicine (TCM) used to treat depression, may improve depression-like behaviour by modulating the gut microbiota. However, the functional groups and mechanisms of action in the XYS treatment of depression remain unknown. This study aimed to analyse with clone sequencing the changes in intestinal butyrate-producing bacteria in XYS-treated chronic unpredictable mild stress (CUMS) rats. We successfully established the XYS-treated CUMS rat model of depression. Rat faecal samples were collected before, during, and after the experiment, and butyryl-CoA:acetate CoA-transferase gene primers were selected for PCR amplification to determine the diversity of butyrate-producing bacteria. The results showed that XYS increased intestinal butyrate-producing bacterial diversity in CUMS rats regarding phylum and genus numbers; the number of phyla increased to two, distributed in Firmicutes and Bacteroides, and four genera were distributed in Eubacterium sp., Roseburia sp., Clostridium sp. and Bacteroides sp. Only one phylum and two genera were present in the model group without XYS treatment. Our findings indicate that XYS can improve depression-like behaviour by regulating intestinal butyrate-producing bacteria diversity, particularly Roseburia sp. and Eubacterium sp., thus providing new insights into the targeted regulation of the intestinal flora to treat depression.