The purpose of this study was to investigate the effects of defatted Schizochytrium sp. as a feed ingredient on the growth performance, lipid metabolism and health status of the indigenous fish, Onychostoma macrolepis. 0 g/kg (DS0), 30 g/kg (DS3), 60 g/kg (DS6), 90 g/kg (DS9) and 120 g/kg (DS12) of defatted Schizochytrium sp. were added to the five isonitrogenous and isolipid feeds, respectively. 180 Onychostoma macrolepis (9.00 g±0.25 g/ind., 12/tank) were fed and cultured in an indoor circulating water system for 56 days. The results showed that: 1) There were no significant differences in weight gain rate (WG), specific growth rate (SGR) and feed conversion ratio (FCR) among the groups (P>0.05); 2) The condition factor (CF), hepatosomatic index (HSI), intraperitoneal fat body index (IFI), and triglyceride (TG) content of liver and intraperitoneal fat in DS9 and DS12 groups were significantly lower than those in the control group (P<0.05); 3) The DHA content, ∑n-3 LC PUFA (n-3 long-chain polyunsaturated fatty acid) content, n-3/n-6 PUFA ratio, cholesterolemia index (h/ H) and lipid quality index (FLQ) were significantly higher than those in the control group, while the atherosclerosis index (AI) and thrombosis index (TI) were significantly lower than those in the control group (P<0.05); 4) The mRNA expression levels of fatty acid synthase (FAS) and acetyl-CoA carboxylase 1 (ACC1) in the liver of all treatment groups were significantly lower than those in the control group (P<0.05); The mRNA expression levels of acetyl-CoA carboxylase 2 (ACC2) and triglyceride hydrolase (ATGL) were significantly higher than those in the control group (P<0.05); 5) The activity of superoxide dismutase (SOD) in the serum of all treatment groups was significantly higher than that of the control group, and the content of malondialdehyde (MDA) was significantly lower than that of the control group (P<0.05). Studies have shown that adding 90 g/kg of defattedSchizochytrium sp. to the diet may significantly reduce the accumulation of abdominal fat and liver fat in Onychostoma macrolepis by affecting the expression of genes related to lipid metabolism, and improve its muscle nutritional value and enhance the body's antioxidant capacity.