The invention discloses a microbial agent for producing nonantigenic soybean meal and a preparation method thereof and belongs to the technical field of microorganism application. The microbial agent uses Bacillus subtilis strain WB117, Saccharomyces cerevisiae Meyenex Hansen strain WY238 and Lactobacillus sp. strain L1 as strains. The strains are prepared into single-strain microbial agents respectively through inoculation, fermentation and culture; and the single-strain microbial agents are blended according a weight ratio of 1-3:1-3:1-3 to form a composite microbial agent. The microbial agent ferments a soybean meal raw material so as to remove antigenic substance and anti-nutritional factors, reduce the toxic action of the soybean meal on livestock, promote digestion and absorption, and improve percentage of the soybean meal in feed and the nutritional value of the soybean meal. The microbial agent and the method can be popularized among and used in feed additive enterprises and livestock farms or peasant households.