Oral probiotic-based therapy has emerged as a promising solution with multifaceted benefits for immunosuppression treatment. However, their widespread and clinical utility is severely limited by the poor viability of probiotics under harsh gastrointestinal conditions in the intestine. To address these challenges, a probiotic-based biohybrid (Lr@DGN) was bio-orthogonally fabricated by covalently anchoring the prebiotic β-glucan (GN) to the probiotic Limosilactobacillus reuteri (Lr). Upon oral administration, Lr@DGN colonized intestines with high survival rates, aided by gastrointestinal stress-shielding of GN, leading to immuno-enhancing effects through combining GN and live Lr. Consequently, in a Cy-induced immunosuppression mouse model, oral administration of Lr@DGN significantly mitigated body weight loss, restored the key immune organ indexes (thymus and spleen), ameliorated Cy-induced damage to the small intestine, enhanced the intestinal immune response, and elevated the serum levels of immunoglobulins IgG and IgA. By integrating the effects of a prebiotic shield and a live probiotic, this biohybrid system offers a promising and translatable approach for managing immunodeficiency and related disorders.