Compared to traditional herbage, functional native herbage is playing more important role in ruminant agriculture through improving digestion, metabolism and health of livestock; however, their effects on rumen microbial communities and hindgut fermentation are still not well understood. The objective of present study was to evaluate the effects of dietary addition ofAllium mongolicumon bacterial communities in rumen and feces of claves. Sixteen 7-month-old male calves were randomly divided into four groups (n= 4). All calves were fed a basal ration containing roughage (alfalfa and oats) and mixed concentrate in a ratio of 60:40 on dry matter basis. In each group, the basal ration was supplemented withAllium mongolicum0 (SL0), 200 (SL200), 400 (SL400), and 800 (SL800) mg/kg BW. The experiment lasted for 58 days. Rumen fluid and feces in rectum were collected, Rumen fluid and hindgut fecal were collected for analyzing bacterial community. In the rumen, Compared with SL0, there was a greater relative abundance of phylum Proteobacteria (p< 0.05) and generaRikenellaceae_RC9_gut_group(p< 0.01) in SL800 treatment. In hindgut, compared with SL0, supplementation ofA. mongolicum(SL200, SL400, or SL800) decreased in the relative abundances ofRuminococcaceae_UCG-014(p< 0.01),Ruminiclostridium_5(p< 0.01),Eubacterium_coprostanoligenes_group(p< 0.05), andAlistipes(p< 0.05) in feces; Whereas, the relative abundances ofChristensenellaceae_R-7_group(p< 0.05), andPrevotella_1(p< 0.01) in SL800 were higher in feces, to maintain hindgut stability. This study provided evidence thatA. mongolicumaffects the gastrointestinal of calves, by influencing microbiota in their rumen and feces.