Two groups of Apostichopus japonicus, a thermotolerant strain (group G3: wet weight, 64.22 ± 13.16 g/ind.), which was selected focusing on the performance of thermo‐tolerance through three generations for 10 years, and a control group (group C: wet weight, 62.08 ± 12.01 g/ind.) were collected from July to October in a seawater pond in northern China. Differences in relative faecal mass (RFM), relative intestinal mass (RIM), percentage of individuals with faeces (PIWF) and intestinal metabolites were investigated and compared between the two groups. The temperatures of terminating aestivation of the two groups were assessed according to the values of RFM and RIM. A regression analysis showed that the corresponding group G3 temperatures were 0.56–1.34°C and 0.70–1.49°C higher than those of group C when RFM and RIM were 0.01–0.05 and 0.005–0.025 respectively. The PIWF values in group G3 were 11.5%–21.2% higher than that in group C from 20 July to 22 September. Significant differences at the concentrations of 52 metabolites were detected between the two groups, 36 were higher in group G3 and 16 were higher in group C. The concentrations of threitol, 2‐methylglutaric acid, N‐acetyl‐D‐galactosamine, N‐acetyl‐L‐leucine, lactose, oxoproline, 2,3‐dimethylsuccinic acid and d‐glucoheptose were significantly different between groups G3 and C and were considered metabolic markers distinguishing group G3 from group C. Metabolism of A. japonicus in group G3 was more active than that in group C. These results provide new insight for understanding ingestion and intestinal metabolism in the thermotolerant strain of A. japonicus under high summer temperature.