An in situ experiment was carried out to estimate the temporal variations in physiological characteristics of the sea cucumber Apostichopus japonicus bottom-cultured in a subtropical fish farm. Results showed that the oxygen consumption rates of the A. japonicus in the fish farm ranged from 0.012 to 0.016 mg O₂/(g·h), and no significant differences were observed between the values at different sampling times (P=0.145). This indicated the energy consumption for the basic metabolic needs of the animals didn't vary obviously during the experiment; however, the oxygen consumption rate of A. japonicus in the reference site during the May sampling was significantly higher than those in February, March and June, which indicated that high energy consumption at the beginning of aestivation. During the February and March samplings, the oxygen consumption rates of A. japonicus in the fish farm were significantly higher than those in the reference site during this period, indicating the higher metabolic rates of the animals in the fish farm. The ammonium excretion rates of A. japonicus in the fish farm decreased with time, and the value at the February sampling[(0.061±0.009) μmol/(g·h)] was significantly higher than those in May[(0.045±0.011) μmol/(g·h)] and June[(0.035±0.007) μmol/(g·h)], because water temperatures in winter and spring were suitable for the growth of A. japonicus, and animals in the fish farm could assimilate more food of better quality from the surrounding environment. A. japonicus in the fish farm underwent aestivation and their guts degenerated after May, and their ammonium excretion rates decreased simultaneously. The ammonium excretion rates of the A. japonicus in the reference site were low and constant during the whole study period, which indicated that animals were always in low nutritional condition. The O/N ratios of both sites ranged between 10 and 30, which indicated the mixed utilization of carbon-based substrates and protein acted as the catabolic substrate for A. japonicus. The O/N ratios of A. japonicus in the fish farm was lower than the reference site from February to May, which demonstrated the protein-dominated catabolism of the animals, and it corresponded to the higher food quality in the fish farm.