The purpose of this test was to study the effects of contents of macromolecular protein and peptide in fermented soybean meal on the intestinal villi structure of piglets, and analysed the contents of macromolecular protein and peptide by gel filtration. Forty weaned piglets were randomly allotted into 4 treatments: dehulled soybean meal treatment, fermented soybean C treatment, fermented soybean E treatment and animal protein treatment. The experiment lasted for 5 weeks. The results showed as follows: the macromolecular protein content in dehulled soybean meal was about 80%, which in fermented soybean meal was about 50%, even down to 24%; the peptide content in fermented soybean meal was about 19%, which in dehulled soybean meal was 2.7%. Compared with the dehulled soybean meal treatment, the villus height in duodenum of fermented soybean C treatment was significantly increased (P<0.05), the crypt depth in duodenum and jejunum of fermented soybean E treatment and fermented soybean C treatment was significantly decreased (P<0.05), the villus height and crypt depth ratio in duodenum and jejunum of fermented soybean E treatment and fermented soybean C treatment was significantly increased (P<0.05). In conclusion, macromolecular protein content in soybean meal is negatively correlated with small intestinal villus height and crypt depth ratio; fermented soybean meal can be used in weaning piglets diets, and effectively improve the structure of small intestinal villus of weaning piglets.