A 1H NMR‐based metabolomics approach was to explore the effect of ultrafiltered fish protein hydrolysate (UF) levels on the liver and muscle metabolic profile of juvenile turbot (Scophthalmus maximus L.). Fish protein hydrolysate (FPH) was produced from by‐products by enzymatic treatment, and UF was obtained by diluting FPH followed filtration. Fish were fed diets containing fish meal protein, which was, respectively, replaced by UF protein 0, 50, 100, 150 and 200 g kg−1 of dietary total protein (UF‐0, UF‐5, UF‐10, UF‐15 and UF‐20) for 68 days. OPLS‐DA of liver and muscle showed that high levels of UF in diets may lead to corresponding tissue metabolites changes. In liver tissue, changing metabolites included dimethylamine, N,N‐dimethylglycine, valine, isoleucine, leucine, arginine and alanine and were mainly involved in choline metabolism and amino acid metabolism. For muscle tissue, changing metabolites included lactate, alanine, proline, fumarate, tyrosine, histidine, cystathionine and taurine. And the metabolites were mainly involved in glycolysis and gluconeogenesis, proline metabolism and taurine metabolism. 1H NMR‐based metabolomics is a useful approach to investigate different levels of UF on metabolic profile in liver and muscle tissues combined with the growth.