To explore the potential probiotic effect of an Enterocin Y3 producing strain of Enterococcus faecalis DH9003， about 15 healthy C57 male mice were intragastrically administered with sterile saline (control group， n=7) and E. faecalis DH9003 (treatment group， n=8). After 4 weeks， the feces of mice were collected to determine the effect of E. faecalis DH9003 on intestinal flora modification and metabolic function of mice. The results showed that E. faecalis DH9003 were colonized in large quantities in mice within 7 days after intragastric administration. The number of the strain increased slowly and became stable at 7-28 days. By observing the pathological characteristics of the intestinal and liver tissue sections of mice， the intake of E. faecalis DH9003 had a certain improvement effect on the intestinal mucosa barrier of mice， indicating that the strain made the intestinal mucosa of mice denser and longer. Meanwhile， the strain showed no pernicious influence on the livers of mice. The intragastric administration of E. faecalis DH9003 led to the different diversity of the treated group， and became the dominant species among different groups. The supplement of E. faecalis DH9003 had a certain regulatory effect on the bacterial community structure modification in the intestinal tract of mice， and the modification at the phylum level was the differences of relative abundance between Bacteroidetes and Firmicutes. A total of 254 differential metabolic substances were detected between control and treatment group， and 124 differential metabolic substances were up-regulated and 130 differential onces in turn were down-regulated. The enrichment analysis of KEGG pathway showed that the metabolic pathways with high levels of visibility included ABC transporter proteins and protein digestion and absorption pathways. In summary， E. faecalis DH9003 could be colonized in vivo and effect on intestinal flora and metabolic ability of the host in some degree.