This study evaluated the effects of a pelleted high-grain total mixed ration (TMR) on rumen fermentation, epithelium-associated microbiota and rumen epithelium health of Hu sheep. Fifteen (15) male lambs were allocated to three (3) dietary groups (n = 5 for each). The first group (CON) received a low-grain non-pelleted TMR; (300 g/kg diet) concentrate, the second group (HG) received a high-grain non-pelleted TMR; (700 g/kg diet) concentrate, while the third group (HP) also received a high-grain TMR in a pelleted form. As compared with the HG group, rumen pH of the HP group was lower (P = 0.012), while lactate concentration was observed to be higher (P = 0.024). The analysis of the molecular variance revealed that all the three (3) groups clustered separately from each other. The alpha diversity estimators (OUT numbers, ACE and Chao) were decreased in the HG group compared with the CON group as well as in the HP group compared with the HG group. Bacteroidetes and Firmicutes were found to be the predominant phyla in all the groups. At the genus level, Prevotella showed a significant increase in the HG group compared with the CON group (P = 0.009) while showing no significant difference between the HP group and HG group. In contrast, the unclassified Lachnospiraceae showed a significant decrease in the HG group compared with the CON group (P = 0.009). Compared with the HG group, Megasphaera (P = 0.008), Rumincoccus (P = 0.016), Olsenella (P = 0.007) and Sharpea (P = 0.005) were significantly increased in the HP group. While, the predominant OTUs that belonged to Prevotella and unclassified Prevotellaceae increased in the HG group as compared with the CON group.The up-regulation of TNF-α and IL-6 in the HG group coupled with the disruption of the stratum corneum as shown in the histological examination indicate the presence of inflammation. In summary, this study showed that feeding of pelleted high-grain TMR to Hu sheep altered the rumen fermentation and epithelium associated microbiome which resulted in rumen epithelial injuries thereby affecting animal production.