Human health is closely related to the gut microbiota. Gut microbiota disorders can lead to various diseases including colitis, food allergy, obesity, and constipation. Prebiotics play an important role in improving the growth of intestinal probiotics and maintaining intestinal homeostasis. Considering that prebiotics play a positive role in regulating the gut microbiota and protecting human health, this paper reviews recent progress in understanding the roles of soybean prebiotics in enriching the intestinal probiotics, inhibiting the intestinal colonization of pathogenic bacteria, improving the production of short-chain fatty acids and the absorption of nutritional substances, enhancing the intestinal immune system, and protecting human health. This review will hopefully provide theoretical guidance for intervening in human health through regulation of the gut microbiota by soybean prebiotics.