BACKGROUND: In intensive aquaculture systems, the frequent incidence of enteritis reduces production efficiency and results in significant economic losses. Protein feeds account for 40%-60% of aquafeed expenses, and with the growth of intensive aquaculture, demand for fishmeal as a key protein source outstrips supply, driving up prices. This study investigated the therapeutic potential of reducing dietary protein levels by 3% and adding enzymatic cottonseed protein (ECP) in juvenile yellow catfish with dextran sulfate sodium (DSS)-induced enteritis. METHODS: A total of 1,260 healthy juvenile yellow catfish (Pelteobagrus fulvidraco), with an average body weight of 5.90 ± 0.05 g, were randomly allocated into 7 experimental groups, each with 3 replicates. The fish were fed one of seven diets for 10 weeks: a normal-protein diet (42%; NP) and 6 low-protein diets (39%; LP) supplemented with graded levels of ECP at 0% (ECP0), 1% (ECP1), 2% (ECP2), 3% (ECP3), 4% (ECP4), and 5% (ECP5), respectively. Subsequently, 48 fish from each group were selected to receive 1 mL of 6% DSS solution. RESULTS: Our findings demonstrated that: (1) The DSS + ECP0 group aggravated DSS-induced enteritis in juvenile yellow catfish compared to the DSS + NP group. (2) Dietary supplementation of ECP in LP diets significantly enhanced the enzymatic activity and levels of immunoreactive substances, including LZM, C3, C4, and ACP (P < 0.05). Mechanistically, first, ECP supplementation modulated macrophage polarization by inhibiting the M1 phenotype while promoting the M2 phenotype, potentially through the JAK-STAT signaling pathway; second, dietary ECP suppressed the phosphorylation cascade of key necroptosis-related proteins, including RIP1, RIP3, and MLKL, potentially via the NF-κB and MAPK signaling pathways. (3) The DSS + ECP2 group demonstrated comparable or superior efficacy to the DSS + NP group in mitigating DSS-induced intestinal enteritis. CONCLUSIONS: Our results demonstrated that ECP can alleviate DSS-induced enteritis by regulating macrophage polarization and reducing necroptosis. Furthermore, ECP supplementation effectively counteracted the exacerbation of enteritis caused by dietary protein reduction. These findings highlighted the effectiveness and feasibility of ECP in alleviating enteritis and saving protein.