Plant-based fermented foods, known for their potential to enhance immunity and improve gut flora, are currently gaining widespread attention. In this study, a patented probiotic (MB11) was employed to ferment soya milk, resulting in the production of probiotic-fermented soya milk (PFS), which was subsequently evaluated for its immunomodulatory effects and impact on gut flora in immunosuppressed mice. Our results demonstrated that PFS significantly bolstered splenic and thymic indicators of immune system health, attenuated small intestinal tissue damage, and promoted the secretion of cytokines and immunoglobulins. Moreover, PFS supplementation led to improved gut flora composition, elevated concentrations of beneficial short-chain fatty acids, reduced relative abundances of pathogenic intestinal bacteria, and boosted numbers of beneficial bacteria compared to the control group. These findings suggest that PFS enhances immunity by modulating gut flora composition, underscoring its potential as a promising immunomodulatory food.