Probiotics play a crucial role in modulating the immune system and maintaining intestinal epithelial barrier integrity. The study investigates the effects of high-activity probiotic yogurt on immunosuppressed mice induced by cyclophosphamide (CTX). ICR male mice (8-week-old) were injected intraperitoneally with CTX (80 mg/kg body weight/day) on days 7, 8, and 9 to establish an immunosuppressive model (n = 10). Mice were fed a normal diet or high-activity probiotic yogurt for consecutive 14 days. The effect of three high-activity probiotic yogurt(109 CFU/250 g, 1010 CFU/250 g, and 1011 CFU/250 g, named as LPY, MPY, and HPY) on immunosuppressed mice was investigated by HE staining, enzyme-linked immunosorbent assay (ELISA), Western blotting, and 16 s rRNA sequencing. Results indicated that high-activity probiotic yogurt significantly increased the immune organ indices, interleukin-6 (IL-6), interleukin-12p70 (IL-12p70), tumor necrosis factor-α (TNF-α), and improved intestinal structure (P < 0.05). Western blotting revealed that high-activity probiotic yogurt improves the expression of toll-like receptor 4 (TLR4), nuclear factor kappa-B-p65 (p65), and TNF receptor associated factor 6 (TRAF6). Furthermore, 16 s rRNA analysis demonstrated that high-activity probiotic yogurt increased the diversity and richness of the gut microbiota, and the effect of LPY performed better than MPY and HPY. These findings indicated that high-activity probiotic yogurt may improve the immune function of mice by improving intestinal homeostasis and activation of the TLR4/NF-κB signaling pathway.