Nutritional values of animal diets depend on the type of oil in the feed ingredient, but the underlying metabolic mechanisms of dietary oil in animal feed have not been thoroughly studied in aquatic animals, especially in crustaceans. In the present study, we conducted assays on GC–MS-based metabolomics and nutritional parameters to investigate the metabolic mechanisms between juvenile Chinese mitten crabs (Eriocheir sinensis) fed olive oil containing 69% oleic acid (OA) and perilla oil containing 56% linolenic acid (LNA). Crab fed OA displayed faster growth, lower concentrations of hepatic glycogen, triglycerides and peroxidation products than those fed LNA. In the metabolomics assay, among 222 peaks isolated, 69 peaks were identified in serum. Among 13 significantly different metabolites between OA and LNA groups, six metabolites related to glycolysis and TCA (tricarboxylic acid) cycle (pyruvate, succinic acid, lactose, malic acid, D-glyceric acid and threitol), methionine, 2-keto-isovaleric acid (intermediate for valine and leucine synthesis) and 2-hydroxybutanoic acid (intermediate for glutathione synthesis) were higher in the OA group than in the LNA group. Only glutaconic acid (intermediate of ketogenic amino acids breakdown) was higher in the LNA group. This study indicates that crab in the OA group increased degradation of glucose and lipids to provide energy for growth as compared with crab in the LNA group. This is the first metabolomics study to identify the key pathways and crucial metabolites as biomarkers to differentiate the metabolic mechanisms of crustaceans fed contrasting dietary oils.