Apostichopus japonicus is an important economic species with a high nutritional value. Aquaculture models have diversified with the rapid development of the sea cucumber industry, resulting in a distinct quality of A. japonicus. In this study, ultra-performance liquid chromatography–quadrupole–time-of-flight mass spectrometry (UPLC-Q-TOF/MS) technology was used to analyse body wall metabolites of cage-cultured, pond-cultured and bottom-sowing A. japonicus. The results were combined with multivariate analysis (PLS-DA) and KEGG to identify the differential metabolites under various aquaculture models. The results revealed that cage-cultured A. japonicus showed a high level of lipid metabolism, including Docosapentaenoic Acid (DPA), Adrenic Acid, Docosahexaenoic Acid (DHA), PC (2:0/19:2). Pond-cultured A. japonicus showed a high level of metabolism of LysoPC 16:1, LysoPC 18:3, LysoPC 20:5, Isoleucine, 3-Dehydroxycarnitine. Bottom-sowed A. japonicus showed a high level of metabolism of Leucenol, Uridine, LysoPC 22:1 and Inosine. KEGG pathway analysis showed that the differential metabolic pathways between cage- and pond-cultured A. japonicus were in lipid metabolism, amino acid metabolism and carbohydrate metabolism. Differential metabolic pathways between cage-cultured and bottom-sowed A. japonicus were in lipid metabolism and nucleotide metabolism. The differential metabolic pathways between pond-cultured and bottom-sowed A. japonicus were in lipid metabolism and nucleotide metabolism. The results of this study provide new knowledge for further understanding metabolic differences of A. japonicus in various aquaculture models. Moreover, the data may provide meaningful guidelines for A. japonicus farming and consumption.