Macrophages play essential roles in generating a tolerogenic resident environment, but the interactions between bacteriophages and their action in macrophage tolerance memory remain unknown. Here, we find that gut bacteriophage exposure induces tolerance immunity via reprogrammed macrophages which significantly enhances protection against bacterial lipopolysaccharide (LPS). Bacteriophage-memory macrophages orchestrate LPS-challenge responses into tolerization or hyperresponsive gene expression clusters in a function-specific manner. The tolerized gene cluster encodes pro-inflammatory cytokines, while the induction cluster is a defense-specific response including anti-inflammatory cytokines, antiviral and antimicrobial effectors, and negative regulators of inflammation. Mechanistically, this augmented defense response is dependent on increased expression of IL-10, but not suppression of pro-inflammatory cytokines. Furthermore, bacteriophages suppressed LPS-induced pro-inflammatory genes by repressing histone acetylation target enhancers that coordinate chromatin accessibility to limit inflammation. Thus, our study identifies the function and mechanism of reprogramming actions for bacteriophage in moderating LPS immune responses.