Chlorogenic acid (CGA), an ester formed between caffeic acid and quinic acid, is one of the most abundant phenolic acids and is widespread in fruits, vegetables, cereals and tuber crops. Therefore, the present study was conducted to test the hypothesis that dietary supplementation with CGA could improve intestinal health and regulate intestinal selected microbiota in weaned piglets. A total of twenty-four piglets (21 d of age) were randomly assigned to one of four groups according to their initial BW and sex and fed a basal diet (control group) or a basal diet containing 250, 500 and 1000 mg kg-1 CGA, respectively. The whole trial lasted for 28 d. Dietary CGA supplementation increased (P < 0.05) the duodenal villous height and villous height : crypt depth ratio, but decreased (P < 0.05) the F/G ratio and duodenal crypt depth when compared with the control group. Meanwhile, an increase (P < 0.05) in the jejunal villous height and in the ileal villous height : crypt depth ratio were also observed in CGA-fed piglets. Supplementation with CGA significantly increased (P < 0.05) the activity of serum GSH-Px and the activities of duodenal GSH-Px and CAT, upregulated (P < 0.05) the expression of OCLN in the duodenum and jejunum, and decreased (P < 0.05) the ileal MDA content when compared to the control group. In addition, an increase (P < 0.05) in the population of Lactobacillus and a decrease (P < 0.05) in the population of Escherichia coli were observed in the colon of pigs fed CGA diets. Furthermore, pigs fed CGA diets had higher (P < 0.05) propionic and butyric acid concentrations in the colon. Altogether, our results provide evidence that dietary CGA is beneficial for preserving intestinal morphological integrity and selectively regulating intestinal microbiota, which can provide a means to improve gut health and growth performance post-weaning.