Ammonium overloading is a common response of aquatic organisms to air exposure during transport. This study elucidated the relationship between ammonium overloading and mortality of crab Portunus trituberculatus. Additionally, we also explored the effects of emersion time and air temperature on ammonium loading and concomitant physiological change. To test the air temperature effect, the crab was exposed to 16, 23 and 30°C in air for 3 h, respectively, and then recovered in seawater at 23°C for 12 h. To test the emersion time effect, crab was exposed to 23°C in air for 0.5 and 3 h, respectively, and then recovered in seawater at 23°C for 12 h. In the control group, crab was always immersed at 23°C. At each time interval (0.5, 1.5 and 3 h during air exposure and 0.5, 2, 4 and 12 h during recovery), ammonium excretion rate, level of total ammonium, total free amino acids and urea concentration in hemolymph and the hepatopancreas enzyme activity involved in detoxifying ammonium were analysed. Results showed that crab mortality was positively related with emersion time and temperature while ammonium loading was lower at 16 and 30°C than at 23°C. For crab experiencing thermal inconsistence of culture media ( i.e., 16 or 30°C), they were higher in ammonium excretion rate and activities of ammonium detoxification enzymes, which may be the reason that they had a lower ammonium loading. Prolonged emersion time (3.0 h vs. 0.5 h) increased the ammonium overloading and the activity of ammonium detoxification pathways in crab. Our results demonstrated that emersion-induced ammonium overloading may not be the main reason leading to P. trituberculatus death during air exposure and subsequent recovery. When the culture medium changed, thermal variation, compared with constant temperature, could reduce ammonium overloading in crab by elevating the activities of ammonium detoxification enzymes and ammonium excretion rate during recovery period.