Objective To explore the inhibitory effect of immune complex (IC) on the signal pathways of high-expressed CD40 and CD80 induced by Toll-like receptor (TLR9) agonist CpG oligodeoxynucleotide (ODN) in B lymphocytes. Methods The mice were intraperitoneally injected with CpG ODN or IC plus CpG ODN, and the spleen CD19⁺ B lymphocytes were sorted by magnetic-activated cell sorting (MACS). The expressions of CD40 and CD80 on the B lymphocytes were detected by flow cytometry. The spleen B lymphocytes were isolated from wild type and immunoglobulin G Fcγ receptor Ⅱb (FcγRⅡb) knockout mice by MACS. After the isolated cells were stimulated with CpG ODN or IC plus CpG ODN in vitro, the phosphorylation levels of related protein kinases were detected in the B lymphocytes by Western blotting. Following CpG ODN stimulation, the B lymphocytes were treated with JNK p38 inhibitor SP600125 (50 μmol/L) or p38 inhibitor SB203580 (20 mg/L), and then the CD40 and CD80 expression levels on the CpG ODN-activated B lymphocytes were detected by flow cytometry. Results IC inhibited CD40 and CD80 expressions on the CpG ODN-activated B lymphocytes in vivo (both P<0.05). IC inhibited the phosphorylation levels of JNK and p38 induced by CpG ODN in B lymphocytes, but did not inhibit them in the B lymphocytes from FcγRⅡb^-/- mice. The CD40 and CD80 expressions on the CpG ODN-activated B lymphocytes were significantly decreased after treated with SP600125 and SB203580 (both P<0.01). Conclusion IC can inhibit the CD40 and CD80 expressions induced by TLR9 agonist CpG ODN through inhibiting the JNK and p38 pathways in B lymphocytes.