The invention discloses a lactobacillus reuteri strain having prebiotics characteristics and the application of the lactobacillus reuteri strain. According to the lactobacillus reuteri strain having the prebiotics characteristics and the application of the lactobacillus reuteri strain, lactobacillus reuteri is named lactobacillus reuteri LR1 and preserved in Common Microorganism Center, China Committee for Culture Collection of Microorganisms on 23, Junly, 2015, the preservation address is No. 3, courtyard No. 1, Beichen West Rd, Chaoyang District, Beijing, and the preservation serial number is CGMCC No. 11154. The lactobacillus reuteri strain is obtained by separating the strains from the interior of intestinal tracts of a healthy animal, the safety is high, the strain has a good acid resistant capability and a good cholate resistant capability, the stress resistance is high, the strain has the great capability of inhibiting common pig pathogenic bacteria, adhesion, to enterocyte, of the pathogenic bacteria can be inhibited through adhesion, competition for place-holding and other approaches, and damage, caused by the pathogenic bacteria, to the enterocyte is reduced; the strain can further promote multiplication of the enterocyte, promote the intestinal tracts of the animal to develop to maturation, and the immune modulation function is further achieved.