The surface macromolecules of probiotic bacteria play crucial roles in modulating immune responses in the host. Exopolysaccharide (EPS) from lactic acid bacteria (LAB) have been widely reported to exhibit immunomodulatory activity. In this study, the EPS biosynthesis gene cluster of Lacticaseibacillus paracasei S-NB was analyzed and a deletion mutant S-NB△7576 (two genes S-NB_2175/wze and S-NB_2176/wzd were responsible for the chain length determination and export of EPS) was successfully constructed, resulting a 40.02% decrease in the production of EPS. The deletion of wze and wzd had little effect on the monosaccharide composition and major groups of the two EPS fractions (BEPS1 and BEPS2). Both BEPS1 and BEPS2 could inhibit the transcriptional level of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) mRNA in RAW 264.7 cells induced by lipopolysaccharide (LPS), and enhance host immune tolerance via suppressing NF-κB and MAPK signaling. Notably, the S-NB△7576 mutant supplied with the BEPS1/BEPS2 exhibited more significant inhibition of cytokines production and the phosphorylation of p65 and c-Jun N-terminal kinase (JNK) in LPS-stimulated cells compared with the S-NB△7576 mutant alone. Our study provided the immunomodulatory effect of BEPS1 and BEPS2 from L. paracasei S-NB, in which the wze and wzd genes associated with EPS biosynthesis may play an important role.