Abstract:[Objective] To investigate the effects of bio-fermented rice straw on intestinal epithelial morphology and microflora of Hu sheep by microscopic observation and 16S rRNA gene high-throughput sequencing technology. [Methods] Twenty-one male lambs aged 70 d with similar body weight (25.15±0.47) kg were randomly divided into three groups based on the composition of dietary roughage, namely, the rice straw group, the bio-fermented rice straw group, and the alfalfa hay group, with dietary concentrate to forage ratio of 6:4. The experiment lasted for 7 weeks, including 3 weeks of the adaptation period and 4 weeks of the experimental period. At the end of the experiment, all animals were sacrificed to collect samples. Epithelial tissues of the rumen, jejunum, and colon were collected for morphological observation. The content of corresponding intestinal segments was collected for the analysis of microbiota and metabolites. [Results] Compared with the rice straw group, the bio-fermented rice straw group significantly increased the relative abundance of Fibrobacteres and the content of volatile fatty acids (VFA) in the rumen of Hu sheep, and promoted the development of the rumen epithelium. The bio-fermented rice straw significantly increased the relative abundance of Firmicutes and Verrucomicrobia in the jejunum of Hu sheep. It changed the structure of the jejunal microbial community and promoted the development of jejunal epithelial tissues. Moreover, the colonic microbial structure of Hu sheep was also changed by the bio-fermented rice straw. [Conclusion] Feeding bio-fermented rice straw is beneficial to the development of intestinal epithelium and increases the microbial diversity in the digestive tract of Hu sheep.