This study examined the effects of low-intensity (L group, 0.4 BL/s), moderate-intensity (M group, 0.8 BL/s), and high-intensity (H group, 1.2 BL/s) exercise on the growth, physiological traits, muscle fiber characteristics, and gut health of large yellow croaker (Larimichthys crocea) in a recirculating aquaculture system (RAS). The results indicated that exercise intensity did not significantly affect the body length, weight, or condition factor of Larimichthys crocea; however, the feed conversion ratio increased significantly with higher exercise intensity. In the low-intensity exercise group (L group), the fish exhibited immune dysfunction and intestinal microbiota imbalance, which heightened the risk of infection and decreased survival rates. In contrast, the moderateintensity exercise group (M) showed elevated antioxidant markers (e.g., SOD, NO) and immune markers (e.g., AKP, AST), while metabolic indices (e.g., GSP, CHO) were significantly lower. These findings suggest that moderate exercise enhances the antioxidant and immune capabilities of large yellow croaker, while simultaneously reducing metabolic stress and improving energy efficiency. Additionally, the digestive function of the gut in the M group was improved, and the intestinal microbiota structure became more balanced, as evidenced by increased villus height and higher abundance of Firmicutes, coupled with reduced abundance of Bacteroidota. Notably, high-intensity exercise (H group) substantially increased the richness and diversity of the intestinal microbiota but also triggered oxidative stress, significantly raising the metabolic burden of the fish. Furthermore, the study revealed that increased flow rate resulted in a significant rise in mitochondrial density and muscle fiber short diameter in the muscle tissue of large yellow croaker, indicating an adaptive response to high-flow environments through muscle structural modifications. These findings provide valuable insights for the development of Larimichthys crocea RAS.