The objective of this study was to investigate the effect of long-term intake of pea fiber (PF) on colonic health and the underlying mechanism. Fifty weaned piglets were randomly allocated into 2 groups receiving control and fibrous diet with inclusion of PF from weaning to Day 160 postweaning, with 5 pens in each group and 5 pigs in each pen. Compared with control diet, long-term intake of PF diet induced deeper crypt and increased colonic barrier-related protein expression of mucin and sIgA. As indicated by the increased lactobacillus content, pigs fed PF diet had a stimulating effect on bacterial fermentation in the colon, thus a higher concentration of colonic total short chain fatty acid and acetic acid were observed. DNA microarray results suggested that feeding PF diet inhibited 77% of genes (40 downregulated and 12 upregulated genes) related to colonic cancer, immune response, and lipid metabolism, involving in signal pathway such as intestinal immune network for IgA production, peroxisome proliferator-activated receptor signaling pathway and nutrient metabolism-related pathways. Collectively, our results suggested that long-term intake of PF would improve colonic function via altering colonic barriers, colonic immune and metabolism-related protein or gene expressions.