Bifidobacterium breve is recognized as an important member of the dominant gut microbiota early in life, playing a crucial role in intestinal immunity. Although B. breve can bioconvert linoleic acid (LA) into conjugated linoleic acid (CLA) to exert immunomodulatory effects, its region-specific immune functions and precise roles in shaping gut microbial composition remain elusive. Our study aimed to evaluate the immunomodulatory effects and microbiota-modulating properties of CLA-producing B. breve strains in lipopolysaccharide (LPS)-induced inflammation model using rat pups. LPS stimulation significantly alters the relative transcriptional levels of inflammatory cytokines in intestinal tissues. Interventions with different B. breve strains demonstrated efficacy in alleviating LPS-induced intestinal inflammation, with B. breve CCFM683 exhibiting particularly broad-spectrum immunomodulatory capacity and comprehensive therapeutic effects. B. breve CCFM683 modulates gut immunity in rat pups via increasing interleukin-10 (IL-10) level and reducing interleukin-1β (IL-1β), interleukin-6 (IL-6), interferon-gamma (IFN-γ) and tumour necrosis factor-alpha (TNF-α) mRNA expression. Furthermore, B. breve CCFM683 administration significantly altered the CLA level in the cecum and colon. Moreover, strain CCFM683 treatment can help restore gut homeostasis and promote beneficial alterations in gut microbiota composition by increasing the abundance of Ligilactobacillus. These results indicated that CLA-producing B. breve can alleviate LPS-induced inflammation, with B. breve CCFM683 had great functionality in regulating the intestinal immune responses.