The effects of pepsin hydrolysis on the β-conglycinin aggregates formed by heat treatment at different pH were investigated. Results showed that fibrils were still observed, whereas the random aggregates were easily to be digested in the simulated gastric fluid. Electrophoresis and molecular weight analysis indicated that large aggregates still existed after pepsin treatment for fibrils. Hydrolysis resulted in changes in the apparent viscosity (ηapp) of 6% fibril solutions. The ηapp at the shear rate range (0–30 s−1) increased in the order of fibrils < fibrils with pepsin for 60 min < fibrils with pepsin for 30 min. Smaller peptide/fibril fragments were generated, and additional aggregates were reformed during the hydrolysis process, as evidenced by thioflavin T and atomic force microscopy images. The native β-conglycinin hydrolysates comprised a mixture of polypeptides enriched in about 47 kDa. These findings would provide valuable information about effects of enzymatic hydrolysis on plant oligometric globulin aggregates.