Fructans such as fructo-oligosaccharides (FOS) and inulin have been reported to directly regulate ileal inflammatory responses in lipopolysaccharide (LPS)-induced endotoxemic mice, without alterations in the colonic microbiota. Firstly, we replicated this model and found that a single gavage of 10 mg g-1 of fructans directly promoted caecal acetate and propionate production. Thus, the previous understanding of microbiota-independent effects of prebiotic fructans in endotoxemic mice has been challenged. In parallel, we performed a daily gavage of 160 mg kg-1 of inulin, xylan, or Dendrobium officinale polysaccharides (DOP) for two weeks prior to LPS injection. The long-term intake of prebiotic fibres reduced the bacterial load in the spleen and mesenteric lymph nodes (MLNs), and in comparison, a single gavage of fructans increased that. However, the long-term intake was unable to improve the short-chain fatty acid (SCFA) synthesis and epithelial barrier function that were impaired by LPS. Notably, the three fibre types consistently reduced the expression of mucin 2 (MUC2) and variously modulated critical mediators (IL-18, IL-22, and HIF-1α) to regulate the host-commensal microbiota interactions in the ileum. In addition, the three fibre types consistently inhibited the inflammatory T helper (Th) cell response in the ileum, while they diversely modulated the peripheral and systemic Th cell responses. Overall, the prebiotic fibres displayed microbiota-related changes in endotoxemic mice, and the potential associations with the in vivo anti-inflammatory effects of prebiotic fibres need further investigation.