This study was to investigate the effects of chitosan-chelated zinc on ileal microbiota, inflammatory response, and barrier function in weaned piglets challenged with Escherichia coli K88. Piglets of the chitosan-chelated zinc treatment (Cs-Zn; 100 mg zinc+766 mg chitosan/kg basal diet, from chitosan-chelated zinc) and the chitosan treatment (CS, 766 mg chitosan/kg basal diet) had significantly increased ileal villus height and the ratio of villi height to crypt depth. CS-Zn group piglets had a higher abundance of Lactobacillus in the ileal digesta, while the abundance of Streptococcus, Escherichia shigella, Actinobacillus, and Clostridium sensu stricto 6 was significantly decreased. The concentrations of propionate, butyrate, and lactate in the CS-Zn group piglets were significantly increased, while the pH value was significantly decreased. Furthermore, the concentrations of IL-1 beta, TNF-alpha, MPO, and INF-gamma in the ileal mucosa of the CS-Zn and the H-ZnO group (pharmacological dose of 1600 mg Zn/kg basal diet, from ZnO) were significantly lower than those of the control group fed with basal diet, and the mRNA expression of TLR4, MyD88, and NF-kappa B of the CS-Zn group was also reduced. In addition, the mRNA expression of IGF-1 was increased, the protein expression of occludin and claudin-1 was enhanced, while the mRNA expression of caspase 3 and caspase 8 was decreased in the CS-Zn group. These results suggest CS-Zn treatment could help modulate the composition of ileal microbiota, attenuate inflammatory response, and maintain the intestinal function in weaned piglets challenged with Escherichia coli K88.