The invention discloses a method for rapidly and efficiently screening antibacterial genes by a bacillus subtilis expression system. The method includes the steps: firstly, inductively expressing resistance genes existing in a plant to build an integrated cDNA (complementary deoxyribonucleic acid) library; secondly, leading the library into bacillus subtilis, and expressing recombinant plasmids by the aid of a secretion expression system of the bacillus subtilis; thirdly, selecting transformants generating lethal effect on the bacillus subtilis; finally, further performing nematode-resistant selection and crude protein bacteriostasis selection to rapidly and efficiently obtain resistance genes, and performing subsequent verification operation. The method is rapid, high in quality, efficient and high in purposefulness, selection operation is relatively simple, and the probability of acquiring positive clone is high.