The sea cucumber Apostichopus japonicus is an economic species mainly distributed along the coast of northern China, south‐eastern Russia, Japan, Republic of Korea and Democratic People's Republic of Korea. Aquaculture industry of A. japonicus has been facing severe challenge of high temperature. In this study, we studied the mRNA expression profiles of eight key metabolic enzymes involved in carbohydrate and amino acids metabolism in A. japonicus under heat stress. The expression of hexokinase, pyruvate kinase and malate dehydrogenase showed downregulated response to heat stress, while the expression of glutamate dehydrogenase, alanine transaminase and branched‐chain aminotransferase showed upregulated response. In addition, the expression of lactate dehydrogenase and glutamate synthase showed no significant difference. We also applied 1H NMR‐based metabolomics to investigate metabolic changes in the intestine tissue of A. japonicus under heat stress, the results of which revealed nine increased and 10 decreased metabolites in the heat stress group. These response genes and metabolites have potential to become markers for identifying severity of heat stress. More importantly, our findings suggest significant links between gene expression and metabolites changing, highlighting regulation networks of carbohydrate and amino acid metabolism in heat‐stressed A. japonicus.