Fermentation is one of the most common-used technologies in food processing. The nutritional value of food can also be maximized to increase the flavor of food. Among them, soymilk is rich in plant protein among food products. But the plant protein is relatively difficult to be absorbed by the human body. Protease-producing strains can be used to treat soy milk. Specifically, the plant protein can be converted into peptides and amino acids for better digestion and absorption rate. The protease-active strains can be screened from the traditional soybean fermented foods, and then serve as the nutrient source for the growth and reproduction of the soybeans. The proteases can be produced more suitable for the soy protein. The unique production process can also be found in the traditional soybean pastes in Northeast China. Specifically, the steamed soybeans are generally fermented to prepare using multiple procedures, such as stir-frying, brick-making, fermentation, and sauce. A long production history can then produce the unique flavor of typical fermented foods. Since manual production is often brewed in individual workshops, the types of fermentation microorganisms vary greatly, depending mainly on the brewing environment. Furthermore, the current fermentation is focused mostly on the Pixian bean paste. Many functional strains have been found in the Pixian bean paste, including the protease-producing strains. And these strains have been applied to functional foods, such as the descending amines and the inhibiting growth of Aspergillus flavus. Taking the Fushun farmhouse soybean paste as the research object, a series of experiments were carried out to screen the protease strains through the hydrolysis circle. Morphological observation was then characterized to identify eight strains with better decomposition of soybean protein. 16S rDNA sequencing as Bacillus included the 1 strain of Bacillus zhangzhouensis, 1 strain of Bacillus velezensis, 2 strains of Bacillus subtilis, 1 strain of Bacillus siamensis, 2 strain of Bacillus methylotrophicus, and 1 strain of Bacillus tequilensis. The screened strains were used for the soy milk fermentation after the safety analysis. The systematic evaluation was performed on the soluble peptide content, amino nitrogen content, hydrolysis degree, and sensory of soymilk before and after fermentation. The results showed that the soluble peptide content of soy milk increased significantly during production. There was the most significant effect of soy milk after treatment with BJ-20, the amino nitrogen and hydrolysis degree of soymilk also changed significantly. Among them, the effect of soymilk treated with BJ-6 was the most significant, with the amino nitrogen increasing by 10.87% and the hydrolysis degree being 23.49%. The sensory evaluation showed that the tissue state of soy milk was significantly improved after treatment. The finding can enrich the bean processing in the diversity of soybean products. A strong reference and theoretical support can also be provided for the soybean health function.