Ellagic acid (EA) contributes to the immunity and anti-oxidant function of body, whereas there are few reports about its effect on the intestinal health and growth performance of broiler chickens. Hence, the present study was arranged to investigate the effect of dietary supplementary with EA on the intestinal barrier function and flora structure of broiler chickens challenged with Escherichia coli K88 (E. coli K88). A total of 216 healthy 1-day-old, Ross 308 broilers with uniform weight were randomly assigned into three treatment groups, six replicates in each group and twelve birds in each replicate. Broilers in the control (CTR) group and E. coli K88 infected group (ETEC) were fed with the basic diet, and 200 mg/kg EA was supplemented into the diet of the E. coli K88 infected group treated with EA (EAETEC). The animal trial had lasted for 42 days, and the outcomes showed that the ADG and ADFI during the animal trial, the jejunal villi height (VH) and the ratio of VH to crypt depth (CD) tended to be decreased with E. coli K88 treated (P< 0.05). Additionally, the level of serum diamine oxidase (DAO) and intestinal malondialdehyde (MDA) were elevated, the activity of intestinal total superoxide dismutase (T-SOD) and glutathione peroxidase (GSH-Px), the mRNA levels in jejunal claudin-1 and occludin were down-regulated with E. coli K88 treated as well as the transcription levels of ileal Mucin-2, aquaporin-3 (AQP-3) and Na+/H+ exchanger proteins-3 (NHE-3) (P< 0.05). In addition, E. coli K88 down-regulated the α-diversity index of cecal flora, the ratio of Bacteroidota to Firmicutes and the relative abundance of Barnesiella were up-regulated and it of Alistipes was descended with E. coli K88 treated (P< 0.05). Beyond that, the content of propionic acid in the cecal chyme was decreased and the amino acid metabolic pathways were inhibited with E. coli K88 challenged (P< 0.05). Additionally, there was a significant positive correlation between the relative abundance of Alistipes and the levels of butyric acid in the caecal chyme and the activity of GSH-Px in the intestine (P< 0.05). Interestingly, dietary supplementary with EA could reshape the intestinal flora structure and alleviate the above negative effects of E. coli K88 on broiler chickens. In conclusion, dietary supplementary with ellagic acid improved the intestinal barrier function and flora structure of broiler chickens challenged with E. coli K88.