The invention relates to a fermentation method for eliminating anti-nutritional factors in soybean meal, which belongs to the technical field of biological fermentation, and the product is particularly suitable for feeding young animals in aquaculture. Its process steps include: a. preparing soybean meal raw materials; b. adding feed water to the raw materials; A microbial strain of an anti-nutritional factor, and the microbial strain is mainly selected from a single strain of yeast, lactobacillus, bacillus subtilis, rhodopseudomonas palustris or a combination thereof; d, temperature-controlled fermentation, fermentation The temperature is 30°C to 55°C; e, Finished product processing. The method of the invention is easy to master, the process is stable, and the directly obtained product eliminates anti-nutritional factors, and is a nutritious, high-quality, low-cost, safe plant-based feed that satisfies the healthy growth of young animals, and can replace bone meal, fish meal and other animals sex feed.