Vibrio harveyi is an opportunistic pathogen among aquatic organisms, which can cause disease and even death of the cultured tiger puffer (Takifugu rubripes). Vaccination is one of the most promising strategies to prevent infection, and potent adjuvant systems are essential to enhance the immunogenicity of inactivated vaccines. CpG-oligodeoxynucleotides (CpG-ODNs) are novel immunopotentiators to induce strong humoral and cellular immunity. In the present study, the survival rate and immune response in the vaccinated individuals of T. rubripes were examined after the treatment with CpG-ODNs to verify its immune enhancement effect as an adjuvant against V. harveyi. After the V. harveyi challenge, the survival rate of puffers in the vaccine group (vaccinated with inactivated Vibrio harveyi), CpG + vaccine group (vaccinated inactivated Vibrio harveyi and treated with CpG), CpG group (treated with CpG), and control group (treated with PBS) was 53.33%, 60%, 36.67%, and 16.67%, respectively. The proliferation index of spleen lymphocytes in the vaccine group (2.13 ± 0.26), CpG + vaccine group (2.62 ± 0.67) and the CpG group (1.74 ± 0.16) were significantly higher than that in the PBS group (1.27 ± 0.18, p < 0.05), respectively. The concentration of cytokines (IL-1β, TNF-α, IL-6 and IL-8), IgM antibodies and non-specific enzymes (SOD and LZM) in the serum of puffers from vaccine group all increased significantly (p < 0.05) after the vaccination with inactivated V. harveyi. More noticeably, the concentration of IL-1β, TNF-α and IgM antibodies in the serum of CpG + vaccine group increased further (p < 0.05), which was 1.28-, 1.31-, and 1.18-fold of that in the vaccine group at 21 d post-vaccination. The results collectively indicated that the inactivated V. harveyi was able to induce both humoral and cellular immune responses of puffer to defend against infection, and CpG-ODNs could further enhance the immune protection of vaccine as a potential immunopotentiator.