The invention relates to a method for preparing health-benefiting fermented soybean meal enriched in small peptides, gamma-aminobutyric acid (GABA), reducing sugar, lactobacillus plantarum and antimicrobial peptide. By utilizing strains of aspergillus oryzae, saccharomyces cerevisiae, bacillus subtilis and lactobacillus plantarum, the small peptides, free amino acids, reducing sugar, GABA and high viable count content in the lactobacillus plantarum in the health-benefiting fermented soybean meal are obtained through the two-stage solid state fermentation method, the small peptides account for 8.01-18 percent, the free amino acids has the content of 80-300mg/g, the reducing sugar reaches 20-80mg/g, the GABA reaches 0.317-0.5mg/g, the viable count content in the lactobacillus plantarum is 2-6.5*1010cfu/g, the antibacterial titer of antimicrobial peptides is 2.0*103-7.0*104 IU/g, and the yield of the health-benefiting fermented soybean meal is 82.03-90 percent. According to the process, the nutrient effect of the soybean meal can be improved, the prepared fermented soybean meal has the antibacterial effect, partial antibiotics can be replaced, the fermented soybean meal is conveniently preserved and saved, the process is simple and feasible, and the fermented soybean meal is green and environment-friendly and has application significance and wide prospect in the feed industry and breeding industry.