The sea cucumber (Apostichopus japonicus) has become increasingly important aquaculture with the rapid expansion of farming in China and its commercial popularity in Asia. Price varies significantly among sea cucumber species, and since visual differentiation is difficult, food fraud is likely to occur. In this study, we report an analysis of body wall metabolites of the sea cucumber (A. japonicus) from different geographical origins in Dalian, Pikou, Jinzhou and Rushan using ultra-high performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC–Q-TOF/MS). The metabolites of sea cumbers of the different geographical origins were assessed using orthogonal partial least-squares discriminant analysis (OPLS-DA) and analysed using KEGG metabolic pathway analysis. The OPLS-DA clearly discriminated the body wall metabolites of sea cucumbers from the four regions. The differential metabolites mainly included amino acids and lipids. The KEGG metabolic pathway analysis showed that lipid metabolism, amino acid metabolism and protein metabolism were closely related to geographical origin. These results can be used to discriminate the geographical origins of A. japonicus.