The effect of soybean peptides from fermented soybean meal on the intestinal immunity and tight junction of broilers was assessed. Roughly, two-stage fermented soybean meal prepared with Bv and Lb (FSBMB+L), which has nearly three times higher soluble peptides than soybean meal (SBM), and reduced galacto-oligosaccharide (GOS) content and allergen protein. The one-stage fermented by Bv (FSBMB) has the highest soluble peptides, while commercial lactic acid bacteria (FSBML) has the highest Lactic acid bacteria count; these were used to compare the differences in the process. Ross308 broilers (n = 320) were divided into four groups: SBM diet and a diet replaced with 6% FSBMB+L, FSBMB, or FSBML. The growth performance was recorded during the experiment, and six birds (35-day-old) per group were euthanized. Analysis of their jejunum and ileum showed that the fermented soybean meal significantly improved the villus height in the jejunum (p < 0.05) and reduced the crypt hyperplasia. The FSBMB group had the highest reducing crypt depth; however, the FSBMB+L group had the highest villus height/crypt depth in the ileum (p < 0.05). In the jejunum, the relative mRNA of CLDN-1 and Occludin increased 2-fold in the treatments, and ZO-1 mRNA increased 1.5 times in FSBML and FSBMB+L (p < 0.05). Furthermore, the level of NF-κB and IL-6 mRNAs in FSBML increased, respectively, by 4 and 2.5 times. While FSBMB, along with FSBMB+L, had a 1.5-fold increase in the mRNA of IL-10, that of NF-κB increased 2-fold. FSBMB+L and FSBMB singly led to a 2- and 3-fold increase in IL-6 mRNA, respectively (p < 0.05). FSBMB and FSBMB+L can also upregulate MUC2 in the jejunum (p < 0.05). In short, using the soybean peptides from two-stage fermented soybean meal can ameliorate the negative factors of SBM and effectively regulate immune expression and intestinal repair, which will help broilers maintain intestinal integrity.