Effects of different concentrations of carbonate alkalinities on oxygen consumption rate, ammonia excretion rate, plasma ammonia content as well as relative gene expression profile of Rh family in gill of Leuciscus waleckii Dybowski fish were studied using closed water flow respiration measurement chamber. Oxygen consumption rate and ammonia excretion rate were significantly inhibited in different alkalinity conditions in comparison with those in control, and the lowest values of them were found at C_A90, which indicated C_A90 may be the alkalinity limit for this species. Contrarily, the plasma ammonia content showed the opposite trend, first increasing, then decreasing, and peaked at C_A90. No significant difference was found for plasma ammonia content when C_A ranged from 0 to 50 mm, indicating this species has evolved to have specific ammonia excretion mechanism and thus helps to maintain the low level of toxic ammonia form. Quantitative real-time PCR showed that Rhcg1 and Rhcg2 out of the four tested genes in Rh family may play an important role in the process of ammonia excretion under high alkaline stress. Energy metabolism (O:N) study found that L. waleckii Dybowski did not consume too much energy to satisfy the energy needs within tolerance range (C_A0-70); however, when the environmental alkalinity was between 90 and 110, the body fat and carbohydrates became the main energy sources to reduce protein consumption, which in turn decreased the poisonous ammonia excretion. This study served to elucidate the ammonia excretion strategy and possible physiological and molecular mechanism of ammonia excretion in L. waleckii Dybowski under high alkaline stress and it may provide evidence for aquaculturing L. waleckii Dybowski species in different carbonate alkaline water bodies.