The present study investigated the blood biochemistry and metabolic profiles of Chinese sturgeons (Acipenser sinensis) reared in semi-intensive traditional aquaculture systems (TAS) and recirculating aquaculture systems (RAS). Results of serum biochemical indices in the RAS group showed that the levels of total protein (TP), albumin (ALB), globulin (GLO), high-density lipoprotein cholesterol (HDL), low-density lipoprotein cholesterol (LDL), cholesterol (CHOL), and alkaline phosphatase (ALP) were higher than those in the TAS group (p < 0.05). TAS group induced significantly higher levels of glucose (GLU), triglycerides (TG), aspartate transaminase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), lactic acid (LD), and blood urea nitrogen (BUN) than RAS group (p < 0.05). Additionally, a total of 3123 metabolites were detected, including 152 up-regulated and 861 down-regulated metabolites, totally 1013 metabolites were significantly different (VIP > 1 and p < 0.05). The analysis of these different metabolites revealed that the top four significantly metabolic pathways (p-value or FDR < 0.05) were neomycin, kanamycin, and gentamicin synthesis, glycerophospholipid metabolism, folate biosynthesis, and phosphatidylinositol signaling system, which are related to aminoglycosides, lipids, and pterin metabolism. There were 28 metabolites enriched in the four metabolic pathways, including 7 different types of antibiotics, 16 glycerophospholipids, and 5 pterins. Overall, Chinese sturgeons reared in TAS showed higher concentrations of 25 metabolites, and only three metabolites with higher significant activities showed in RAS, including PE (18:1(9Z)/22:6 (4Z, 7Z, 10Z, 13Z, 16Z, 19Z)), PC (14:0/P-18:1(9Z)), and Folic Acid. In conclusion, our results revealed differences in the biochemical indices, metabolites, and metabolic pathways of Chinese sturgeons reared in TAS and RAS and confirmed that RAS improves fish metabolism and physiological state, providing new insights for sturgeon aquaculture.