The immunomodulatory effect of oligochitosan has been demonstrated in several fishes. However, the underlying mechanisms of oligochitosan (OCS) on immune regulation responses are not well characterized. Here, to investigate the effect of OCS on the non-specific immunity and the mechanism of action in Epinephelus fuscoguttatus(♀)×E. lanceolatu (♂), the feeding trial in this study was conducted in quadruplicates with the control diet supplemented with OCS at different concentrations (0, 200, 400 and 800 mg/kg) for four weeks, in order to explore the effects of OCS on the immunomodulation of grouper. Subsequently, the effects of OCS on the immune and antibacterial enzyme activities were examined. The results showed that feeding OCS could significantly improve the enzymatic activities of glutathione peroxidase, lysozyme, catalase, alkaline phosphatase, glutamate transaminase and glutamate transaminase in grouper, but had no significant effect on superoxide dismutase. The addition of OCS could significantly increase the weight of the head kidney of grouper. Quantitative real-time PCR (qRT-PCR) was used to further address the immunomodulation stimulated by OCS, the results showed that the expression levels of IL-6 and IL-1β were significantly up-regulated from head kidney by the addition of lower concentrations of OCS, by contrast, addition of higher concentration of OCS inhibited the expression of IL-6, IL-1β and TNF-α via NF-κB pathway. It means that OCS has a bidirectional effect on inflammation in the grouper. The immunoprotective effect of OCS on grouper was detected by the Vibrio harveyi challenge test. When the groupers were challenged with V. harveyi, the H. E staining results showed that the morphology of head kidney in groupers fed with different concentrations was greatly improved compared with the control group, especially in 800 mg/kg OCS concentration group. Also inflammatory cytokines such as IL--6, TNF-α, IL--1β and NF-κB pathway genes significantly declined in qRT-PCR from kidney of groupers, indicaing that OCS could inhibit the inflammation response of mRNA expression inflammatory factors via NF-kB signaling pathway. Additionally, it significantly inhibited the expression of apoptosis-related genes like Fas, FADD, Bax and Caspase-3 activity. Taken together, appropriate addition of dietary OCS could improve the growth and innate immunity of grouper so as to play a role in the immune protection of the grouper against the infection of V. harveyi. Our results shed a new light on the application of OCS in aquaculture, and paved a new way for the prevention and control of the diseases of grouper.