The invention relates to the technical field of bean food processing, and particularly relates to a process for fermenting stinky preserved soybeans. The process comprises the following steps: washing high-quality soybeans, drying in the air, roasting, soaking, and mixing with little yellow croaker to ferment for 5-7 days in a sealed condition; separating soybeans from little yellow croaker, steaming, inoculating one or more of aspergillus niger, rhizopus oryzae and glucoamylase in the steamed soybeans, seasoning the fermented soybeans, filling into cans, and pasteurizing to obtain a finished product. The stinky preserved soybeans prepared by the process have unique flavor and mellow taste, and can be used for promoting elimination of heavy metals in a body. According to the stringy fermented soybeans, the protein is increased by 30-35 percent, the total amino acid is increased by 22-26 percent, the large molecular weight protein degradation rate is more than 99.2 percent, and the small molecular protein is more than 50.1 percent of soluble protein. The stinky preserved soybeans can be stored for 8 months at normal temperature when chemical preservative is not added.