The aim of this study was to investigate the effects of ensiled agricultural byproducts from Qinghai-Tibet plateau on growth performance, rumen microbiota, ruminal epithelium morphology and nutrient transport-related gene expression in Tibetan sheep. Fourteen male Tibetan sheep were randomly assigned to one of two diets: an untreated diet (without silage inoculum, CON, n=7) or an ensiled diet (with silage inoculum, ESD, n=7). The total experimental period lasted for 84 days, including early 14 days as adaption period and remaining 70 days for data collection. The ESD increased average daily gain (ADG, P = 0.046), dry matter intake (P < 0.001), ammonia nitrogen (NH3-N, P = 0.045), microbial crude protein (MCP, P = 0.034) and total volatile fatty acids (VFA) concentration (P < 0.001), and decreased ruminal pH value (P = 0.014). The proportion of propionate (P = 0.046) and the copy numbers of bacteria (P = 0.01) and protozoa (P = 0.002) were higher, while the proportion of acetate (P = 0.028) was lower in the sheep fed ESD compared to CON. Pyrosequencing of the 16S ribosomal RNA gene revealed that ESD increased the relative abundance of Firmicutes, Ruminococcus, Lachnospiraceae_AC2044_group, Lachnospiraceae_XPB1014_group, Christensenellaceae_R-7_group in the rumen (P < 0.05), while decreased the relative abundance of Bacteroidota, Prevotellaceae_UCG-003, and Veillonellaceae_UCG-001 (P < 0.05). Analyses with PICRUSt2 and STAMP indicated that the propionate metabolism pathway was enriched in the sheep fed ESD (P = 0.026). The ESD increased the rumen papillae height (P = 0.012), density (P = 0.036), and surface area (P = 0.001), and improved the thickness of the total epithelia (P = 0.018), stratum corneum (P = 0.040), stratum germinativum (P = 0.042), and stratum spinosum and basale (P = 0.004). The relative mRNA expression of Cyclin-dependent Kinase 2 (CDK2), CyclinA2, CyclinD2, zonula occludens (ZO-1), Occludin, monocarboxylate transporter isoform 1 (MCT1), monocarboxylate transporter isoform 4 (MCT4), sodium/potassium pump (Na+/K+-ATPase), and sodium/hydrogen antiporter 3 (NHE3) were higher in the rumen epithelial of sheep fed ESD than CON (P < 0.05). Conversely, the relative mRNA expressions of Caspase 3 and B-cell lymphoma-2 (Bcl-2) were lower in the sheep fed ESD than CON (P < 0.05). In conclusion, compared with untreated diet, feeding an ensiled diet altered the rumen microbial community, enhanced nutrient transport through rumen epithelium, and improved the growth performance of Tibetan sheep.