Newborn goat kids exposed to environmental stress are susceptible to diarrhea due to immature intestinal functions and undeveloped gut microbiota. Butyrate-producing bacteria as next generation probiotics benefit the maintenance of intestinal health, but the mode of regulation is still unclear. Herein, a novel butyrate-producing strain was isolated from sheep rumen and identified as Clostridium beijerinckii R8 (C. beijerinckii), thereafter goat kids were treated with C. beijerinckii R8 to elucidate its regulatory mechanisms on diarrhea. Thirty-six goat kids were assigned to four groups: control (CON), low dose (LCB), middle dose (MCB), high dose (HCB) with addition of C. beijerinckii. The experiment lasted for 15 d, and 6 goat kids were randomly selected from each group for slaughter on the last day of the trial. The results showed that this isolate reduced the diarrhea rate (P < 0.001) and fecal scores (P < 0.001). In the gut, its supplementation inhibited inflammation, increased antioxidant capacity, and regulated intestinal flora. Meanwhile, C. beijerinckii R8 strengthened the intestinal barrier and altered the jejunum morphology. This evidence suggests that C. beijerinckii R8 may alleviate diarrhea in goat kids by regulating microbiota, which is directly related to intestinal barrier and immune capacity.