Probiotics have become promising strategies for treating intestinal barrier dysfunction. However, the mechanisms by which probiotic bacteria interact with host cells to elicit beneficial effects remain unclear. Herein, we demonstrate that administration of E. coli Nissle 1917 (EcN) before Salmonella Typhimurium (STm) infection significantly suppressed STm pathogenesis in a mouse model. To address how bacterial interactions with intestinal epithelium affect STm infectivity, we developed a human gut-on-chip model coupled with computational fluid dynamics simulations, which recapitulated in vivo intestinal barrier protective phenotypes under physiologically relevant flow conditions. Using quantitative proteomics, we discovered that EcN-derived outer membrane protein MipA mediates protection by directly binding to intestinal epithelial integrin, inducing upregulation of integrin-linked kinase (ILK) to strengthen tight junctions and block STm invasion. Notably, expression of MipA in non-pathogenic STm conferred comparable barrier protection, establishing its pivotal role as a barrier enhancer. Our finding uncovers a novel mechanism whereby the bacterial membrane protein acts as a molecular trigger to enhance intestinal epithelial integrity, providing a significant framework for probiotic interventions against enteric infections.