The invention discloses a clostridium welchii disease resistant transgenic plant vaccine and a preparation method thereof. At present, the protective ratio on immunization of clostridium welchii disease resistant vaccines is lower. The preparation method of the clostridium welchii disease resistant transgenic plant vaccine comprises the steps of: (1) with a plasmid or disease sample containing coded clostridium welchii toxin as a template, carrying out PCR (Polymerase Chain Reaction) or RT-PCR (Reverse Transcription-Polymerase Chain Reaction) amplification to obtain a clostridium welchii toxin gene, carrying out enzyme cutting on the obtained clostridium welchii toxin gene or the Ti or Ri plasmid respectively, recycling a target gene and a plant expression vector segment, connecting with and converting escherichia coli, carrying out enzyme cutting, PCR and sequencing identification on the recombinant Ti or Ri plasmid, converting agrobacterium tume faciens or agrobacterium rhizogene with the recombinant plasmid, and screening and identifying positive recombinant agrobacterium; and (2) carrying out vernalization, germination and splicing on plant seeds to obtain explants, infecting the explants respectively with the recombinant agrobacterium in the step (1), carrying out screening, subculturing, rooting and transplanting on the infected explants to obtain transformed plants, and screening and identifying positive transgenic plants.