Red yeast rice (RYR), a traditional Chinese fermented food, has the effect of lowering blood lipid and cholesterol, but little information is available about whether RYR can inhibit pathogenic bacterial infection in vivo. The present study explored the effect of RYR on Salmonella enterica-induced intestinal inflammation and gut microbiota dysbiosis in mice as well as the underlying anti-inflammatory mechanism. Results showed that RYR can alleviate S. enterica infection in vivo and Monascus pigments are the main functional components. The analysis of microbiota, gene expression profile and serological immunology revealed that RYR can regulate the intestinal flora and increase the relative abundance of beneficial bacteria such as Lactobacillus and Akkermansia. Meanwhile, RYR is also found to regulate the expression of pro-inflammatory factors and tight junction-related genes to inhibit the NO and NF-κB-mediated inflammatory response and maintain the integrity of the intestinal barrier. This study provides a new dietary intervention strategy for the prevention of pathogenic bacterial infection.