Oligochitosan (OCS) has many important physiological functions, however, the underlying mechanisms on immune regulation of groupers are not well characterized. A feeding trial was conducted in triplicates with the control diet supplemented with OCS at different concentrations (0, 200, 400, 800 and 1600 mg/kg). The effects of OCS on the grouper growth, immune responses and gut microbes were explored after juvenile hybrid groupers [Epinephelus fuscoguttatus (♀)× E. lanceolatu (♂)] were cultured for 4 weeks. The results showed that OCS significantly increased weight gain rate and decreased feed coefficient of hybrid groupers, but had no significant effect on condition factor and survival rate. To elucidate the immune responses stimulated by OCS using qRT-PCR, the mRNA expression levels of inflammation-associated cytokines (TNF-α, IL-1β, TGF-β1, TOR, and TLR3) from midgut were all significantly up-regulated in the 800 mg/kg group compared to the control. At the same time, OCS significantly improved the antioxidant capacity by increasing the expression of GPx, CAT and MnSOD while they also significantly increased the expression of tight junction proteins (ZO-1, ZO-2, ZO-3, and Claudin-3α). To characterize the gut bacterial flora by high-throughput sequencing of 16S rRNA, microbe samples were collected from the foregut, midgut, and hindgut, respectively. We found that although there was no significant differences in the relative abundance and α diversity of intestinal bacterial dominant groups between the OCS and the control group, the abundance of probiotics were increased in the 800 mg/kg group. Additionally, the results of principal coordinate analysis showed that β diversity of bacterial community in 800 mg/kg group was significantly different from that in control group, which indicated that OCS could alter the bacterial assembly of hybrid groupers. To further test the antibacterial ability of hybrid groupers fed with OCS, when the hybrid groupers were challenged with Vibrio harvey, intestinal morphology was greatly improved and the mortality rate of groups fed with 800 m/kg OCS was significantly lower than that of the control. Taken together, appropriate dietary OCS could improve the growth, immune responses and change the bacterial assembly in the gut of hybrid groupers, so as to play a role in the bacterial resistance.