To study the effects of L-Arginine (Arg) on immune responses and intestinal structure in a hybrid grouper (Epinephelus fuscoguttatus ♀× Epinephelus lanceolatus ♂), intraperitoneal injection of different Arg doses (0, 50, 100, 200 mg per kg body weight of grouper) was administered once every seven days, repeating the process three times in the present study. A total of 216 groupers (initial weight of 349.42 ± 0.67 g) were randomly divided into four groups with three replicates, and each of the replicates comprised 18 fish. Serum was sampled at the seven, 14, and 21 days post-injection. The results showed that injection of Arg had a significant effect on serum albumin, immunoglobulin M (IgM), total protein (TP) and nitric oxide (NO) content, as well as nitric oxide synthase (NOS) and lysozyme activity (P < 0.05). With an increase of Arg dose, serum NO, TP, and albumin levels initially increased and subsequently decreased, and were significantly higher in fish injected with Arg at doses of 50 and 100 mg/kg in comparison to the control group. On days seven and 14, the highest serum albumin, TP, and IgM levels were observed in the 100 mg/kg group. With an increase in injection time and frequency, the 50 mg/kg group showed the optimal immune status after the third injection. Based on the results of the intestinal digestive enzyme activity and morphology, the injection of Arg at 50 mg/kg was the most beneficial, followed by the 100 mg/kg dose. Injection of 200 mg/kg Arg, especially after three injections, had adverse effects on immune responses and intestinal structure. These findings indicated that the intraperitoneal injection of L-Arg at a certain concentration can enhance the immunity and intestinal morphology of groupers. Notably, the most significant benefits were observed after three consecutive injections of Arg at 50 mg/kg in this experiment.