<p>To investigate the response of fish intestines to different culture modes, we conducted a comparative trial on rockfish in the recirculating aquaculture system (RAS) and offshore aquaculture net pen system (OAS). After the 152-day trial, we compared the differences in growth performance, antioxidant capacity, intestinal morphology, and intestinal microbiota to evaluate the health status of rockfish cultured in these two modes. Results showed that rockfish cultured in the RAS exhibited a superior growth performance and antioxidant capacity compared to those cultured in OAS. Histological examination indicated pathological lesions in the intestine of rockfish cultured in the OAS, including a disordered arrangement of epithelial cells, rupture of chorionic villi, and decreased thickness of the muscle layer, which may further cause damage to intestinal barrier function. Sequencing analysis of 16S rDNA showed that Firmicutes, Bacteroidota, and Proteobacteria were the dominant phyla in the rockfish intestines. Microbial community diversity analysis indicated that there were significant differences in intestinal bacterial richness and diversity between the two groups; however, no differences were observed in the dominant bacteria. The relative abundance of metabolic pathways (such as energy, carbohydrate, and lipid metabolism) in the OAS group was significantly enhanced. Furthermore, the relative abundance of conditional pathogenic and potentially pathogenic bacteria increased, and that of beneficial and stress-tolerant bacteria decreased in the OAS group, indicating potential inflammation in the intestine. This study accumulated basic biological information for the study of fish welfare cultured in different modes and will contribute to the understanding of the physiological and health status of the rockfish.</p>