The present invention relates to the fields of immunology and molecular biology and related to a B7-1-PE40KDEL exotoxin fusion gene-based DNA vaccine and the use thereof. Specifically, the DNA vaccine contains a recombinant expression vector, and the vector contains exotoxin fusion gene B7-1-PE40KDEL, which is effectively ligated into selected eukaryotic expression vectors, such as pcDNA3.1/Zeo(+), pWLNEO, pSV2CAT, pOG44, pXT1, pSG, pSVK3, pBPV, pMSG, pSVL, and adenovirus. The invention also relates to the exotoxin fusion gene B7-1-PE40KDEL, the encoded exotoxin fusion protein, a recombinant expression vector that contains the exotoxin fusion gene, and compositions that contain the recombinant expression vector. The DNA vaccine in this invention has a good effect on the treatment or prevention of allogeneic tissue/organ transplant rejection and hematopoietic stem cell transplantation rejection such as GVHD.