The aim of this study was to demonstrate the effect of arabinoxylan on colonic mucosal barrier and metabolomic profiles in high‐fat diet‐induced rats. A total of 20 six‐week‐old male rats were arranged randomly to two groups ( n = 10/group), including a high‐fat diet (HFD) group and a high‐fat supplemented with arabinoxylan diet (AXD) group. Results showed that feeding AXD reduced serum lipopolysaccharide in rats after 5 weeks. In colonic digesta, Escherichia coli population was reduced, while Lactobacillus , Bifidobacterium, and Bacteroidetes populations were increased in AXD group. Metabolomics assay found that the different abundances of 84 metabolites were observed, involving lipid, carbohydrate, and nitrogenous metabolism in colonic digesta. In colonic mucosa, AXD up‐regulated gene level of tight‐junction‐related proteins. Meanwhile, lower TNF‐α and IL‐1β levels were related to TLR4/NF‐κB/MyD88 pathway in AXD group. In conclusion, arabinoxylan could change colonic microbial metabolism and improve the colonic mucosal barrier via modulating intestinal microflora and tight junction proteins.