The current global status of freshwater resources and deterioration of water quality in general have led to limitations on the scope of freshwater aquaculture. The development of technology that would enable aquaculture under saline-alkaline conditions would be valuable. Therefore, the exploration is needed to understand the damage mechanism of saline-alkaline water, particularly the impact of alkalinity, on fish and shellfish. In this study, Chinese mitten crabs (Eriocheir sinensis) were subjected to different concentrations of carbonate alkalinity (0.00, 4.38, 8.75, 17.50, and 35.00 mmol/L) for 96 h. The survival rates in the 17.50 and 35.00 mmol/L alkalinity groups showed a significant decrease compared to the control group and the groups exposed to lower carbonate alkalinity concentrations (4.38 and 8.75 mmol/L). The exposure to carbonate alkalinity had a significant inhibitory effect on the ammonia excretion rate and led to an increase of ammonia content in hemolymph. However, in contrast to the low carbonate alkalinity exposure groups (4.38 and 8.75 mmol/L), the high carbonate alkalinity exposure group (35.00 mmol/L) exhibited a significant reduction in the concentrations of ammonia and urea nitrogen in hemolymph. Moreover, high carbonate alkalinity exposure was found to induce oxidative stress, as indicated by increased levels of reactive oxygen species (ROS) and malondialdehyde. Additionally, there were notable alterations observed in the activities of antioxidant enzymes such as superoxide dismutase, catalase, and glutathione. Flow cytometry analysis and ultrastructural observations revealed that exposure to carbonate alkalinity can induce apoptosis. In the 8.75, 17.50, and 35.00 mmol/L alkalinity groups, the activation of p38 and JNK pathways was observed, along with an increase in the Bax/Bcl-2 ratio and the expression of caspase 3. In summary, the findings of this study suggested that exposure to carbonate alkalinity can disrupt ammonia metabolism, leading to apoptosis through the activation of the ROS/MAPK signaling pathway. This ultimately results in a decrease in the survival rate of crabs. These results provide valuable insights into the toxicological effects of high carbonate alkalinity exposure and shed light on the tolerance mechanisms of high carbonate alkalinity exposure in crabs.