The present study was conducted to investigate the effects of early transplantation of the faecal microbiota from Tibetan pigs on the gut development of dextran sulphate sodium- (DSS-) challenged piglets. In total, 24 3-day-old DLY piglets were divided into four groups (n=6 per group); a 2×2 factorial arrangement was used, which included faecal microbiota transplantation (FMT) (from Tibetan pigs) and DSS challenge. The whole trial lasted for 55 days. DSS infusion increased the intestinal density, serum diamine oxidase (DAO) activity, and colonic Escherichia coli count (P<0.05), and decreased the Lactobacillus spp. count and mRNA abundances of epidermal growth factor (EGF), glucagon-like peptide-2 (GLP-2), insulin-like growth factor 1 (IGF-1), occludin, mucin 2 (MUC2), regeneration protein IIIγ (RegIIIγ), and interleukin-10 (IL-10) in the colon (P<0.05). FMT increased the Lactobacillus spp. count and mRNA abundances of GLP-2, RegIIIγ, and IL-10 in the colon (P<0.05), and decreased the intestinal density, serum DAO activity, and colonic E. coli number (P<0.05). In addition, in DSS-challenged piglets, FMT decreased the disease activity index (P<0.05) and attenuated the effect of DSS challenge on the intestinal density, serum DAO activity, and colonic E. coli number (P<0.05). These data indicated that the faecal microbiota from Tibetan pigs could attenuate the negative effect of DSS challenge on the gut development of piglets.