This study examined the impact of different exercise intensities on the growth performance, serum biochemistry, liver antioxidant capacity, and intestinal health of common carp (Cyprinus carpio). A total of 270 common carp with an initial weight of 63.91 ± 1.45 g were divided into three groups: a Sustained Exercise group [SE, 1 bl/s (body length per second), 24 h/day], an Intermittent Exercise group (IE, 1 bl/s, 8 h/day), and a Control group (CG, 3 cm/s) for a 90-days experiment. The results demonstrated that exercise substantially improved weight gain rates in common carp. Analysis of serum biochemical parameters revealed that increased exercise intensity significantly reduced levels of triglycerides (TG), total cholesterol (T-CHO), and glucose (GLU) (P < 0.05). Post-exercise evaluations also indicated significant reductions in immune-related markers, including lysozyme (LZM), aspartate aminotransferase (AST), and alanine aminotransferase (ALT). Regarding liver antioxidant enzyme activities, the levels of glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) were significantly higher in the IE group relative to the CG group (P < 0.05). Conversely, the total antioxidant capacity (T-AOC) was significantly lower in the SE group than in the CG group (P < 0.05). In terms of intestinal health, intermittent exercise significantly reduced the expression of pro-inflammatory cytokine genes and increased gut villus length. Additionally, an increase in exercise intensity significantly enhanced the activities of intestinal amylase and lipase. Analysis of the intestinal microbiota through 16S rRNA sequencing revealed that intermittent exercise fostered a more diverse microbial community. Specifically, with an increase in exercise intensity, the relative abundance of Fusobacteriota rose, while those of Firmicutes decreased. At the genus level, the abundances of Cetobacterium and Aeromonas increased, contrasting with declines in Muribaculaceae, Bacteroides, and Escherichia-Shigella. PICRUSt2 functional predictions suggest that exercise might modify the intestinal environment by increasing the prevalence of pathogenic bacterial communities, potentially leading to intestinal damage and adversely affecting the physiological state of the intestine. An observed increase in riboflavin metabolism in the SE group likely contributed to its markedly improved growth performance relative to other groups. In summary, sustained exercise at 1 bl/s improved growth and intestinal digestive enzyme activity in common carp. However, it also induced stress, potentially compromising physiological health, liver function, and immune strength, consequently elevating the risk of disease. These findings provide crucial insights for optimizing growth and physiological health in common carp and other fish species in recirculating aquaculture systems through exercise.