We investigated the effects of low and high doses of 7S and the ameliorative effects of NaB (based on high-dose 7S) on the growth performance, serum immunity, distal histopathology, and CIITA-mediated MHC II-PI3K/Akt/mTOR pathway in hybrid groupers. The results revealed that the specific growth rate of groupers significantly increased, decreased, and increased in the low-level 7S (bL), high-level 7S (bH) high-level 7S plus NaB (bH-NaB) groups, respectively. The feed coefficient ratio was significantly increased in the bH and bH-NaB groups, whereas serum levels of IFN-γ, IL-1β, and TNF-α were upregulated in the bH group. The intestinal diameter/plica height ratio was significantly increased in the bH group. Furthermore, there were increases in nitric oxide, nitric oxide synthase (NOS), and peroxynitrite anion (ONOO−) in the bH group, and decreases in NOS and ONOO− in the bH-NaB group. The mRNA levels in distal intestine of TSC1, mTOR C2, CIITA, and CREB1 were significantly upregulated in all three treatment groups, whereas those of IKKα, Rheb, mTOR C1, mLST8, EIF4B, NFY, GILT, and AEP were upregulated and downregulated in the bH and bH-NaB groups, respectively. These indicate 7S has a regulatory effect on serum immunity and affect distal intestinal development by modulating hindgut injury-related parameters. Within the distal intestinal tract, 7S can induce intestinal inflammation by activating the CIITA-mediated MHC II-PI3K/Akt/mTOR pathway, which eventually manifests as a reduction in growth performance. Supplementing feed with NaB represents an effective approach for enhancing serum immunity, and also protects the intestines from damage caused by high-dose 7S.