Chitosan oligosaccharide (COS) is a potent immunopotentiator, but rarely used in aquaculture. The aim of this study was to investigate the effect of feeding frequency with COS once every 3 days on growth, non-specific immune indices, digestive enzyme activities, histological and disease resistance of sea cucumber Apostichopus japonicus. Sea cucumbers (mean body weight 18.51 ± 0.28 g) were first fed for 8 weeks by two groups (control group, sea cucumbers were fed with basal diet; treatment group, sea cucumbers were first fed with basal diet added 0.5% COS for 1 day and then fed with basal diet for 2 days). Growth performance, non-specific immune enzyme activities, intestinal enzyme activities, the structure of the respiratory tree, intestines and immune response were measured to investigate the effects of feeding frequency with COS once every 3 days of sea cucumber A. japonicus. The results indicated that no significant difference was observed in the specific growth rate (SGR) and survival rate (SR) among two groups (P > 0.05), but treatment group had significantly higher ratio of visceral weight to body wall weight (VBR) and ratio of intestine weight to body wall weight (IBR) (P < 0.05). Phagocytic activity and respiratory outburst of coelomocytes in treatment group were significantly higher than those in control group (P < 0.05). The activities of enzymes such as acid phosphatase (ACP), falkaline phosphatase (AKP), lysozyme (LZM) and total nitric oxide synthase (T-NOS) of coelomocytes and intestine in treatment group increased significantly (P < 0.05) and the activities of AKP and LZM of intestine in treatment group increased by 0.70-fold and 1.56-fold, respectively. The relative expression level of acp gene, akp gene, lzm gene (P < 0.05) of intestine in treatment group were significatly higher than that in control group and the relative expression level of akp gene and lzm gene of intestine in treatment group increased by 0.13-fold and 0.22-fold, respectively. The activity of catalase (CAT) of coelomocytes in treatment group was significantly higher than that in control group (P < 0.05), but the content of malondialdehyde (MDA) of coelomocytes and intestine had no significant difference between the two groups (P > 0.05). Compared with the control group, the muscularis and serosa in foregut, fold height and fold width in midgut and hindgut were significantly increased in treatment group (P < 0.05). We found that after the infection with Vibrio splendidus, the survival rate of the sea cucumber A. japonicus increased. Above all, the feeding frequency with COS once every 3 days will be suggested to promote the growth performance, non-specific immunity and immune response of the sea cucumber, and provides theoretical support for follow-up research.