Abstract: To investigate the effect of cysteine on the metabolic disorders of juvenile Trachinotus ovatus (10.05±0.05) g caused by low fishmeal, we prepared a basal pomfret diet by using plant and animal proteins (Chicken meal, soybean protein concentrate, fermented soybean meal, etc.) as partial substitutes for fishmeal, and then added 0 (Group C0, control group), 0.30% (Group C1), 0.60% (Group C2), 0.90% (Group C3) and 1.20% (Group C4) cysteine to make five isonitrogenous and isoenergetic diets. The results of a 56-day feeding trial show that: 1) Cysteine enhanced the protein synthesis and metabolism ability of T. ovatus by activating the S6K/PI3K/TOR/4E-BP1 pathway. Supplementation with 0.6%−0.9% cysteine up-regulated the mRNA levels of ribosomal protein S6 kinase (S6K), target of rapamycin (TOR), phosphoinositide 3-kinase (PI3K) and eukaryotic initiation factor 4E-binding protein 1 (4E-BP1) in muscle, increased total protein (TP) in muscle and serum as well as muscle crude protein content, reduced serum ammonia (SA) and urea nitrogen (UN) in muscle and liver, promoting protein deposition in muscle. 2) Supplementation with 0.6%−0.9% cysteine inhibited lipid anabolism by down-regulating the expression level of peroxisome proliferator-activated receptors gamma (PPARγ) in muscle, decreasing the transcript level and enzyme activity level of Acetyl-CoA carboxylase (ACC) and fatty acid synthetase (FAS), while it up-regulated the expression level of peroxisome proliferator activated receptors-alpha (PPARα) in muscle, resulting in high hormone-sensitive lipase (HSL) and carnitine palmitoyl transferase 1 (CPT1) expression with increasing enzyme activity, which in turn promoted β-oxidation of fatty acids in muscle, reducing protein consumption due to catabolism for energy supply. Thus, protein deposition in muscle is promoted.