High carbonate alkalinity in saline-alkaline water is considered a crucial factor that affects the survival of crustaceans. However, the information regarding the saline-alkaline adaptation mechanisms of Macrobrachium rosenbergii is currently limited. This study aimed to investigate the effects of saline-alkaline stress on the survival, enzyme activity, and transcriptomic profiling of M. rosenbergii by determining its semi-lethal concentration (LC₅₀) and lowest observed effect concentration (LOEC) of salinity and carbonate alkalinity for its larvae. Additionally, the study examined the effects of saline-alkaline stress on osmoregulation, antioxidant enzyme activities, and transcriptional expression in the gills and hepatopancreas of M. rosenbergii. Results showed that the 96 h-LC₅₀ of salinity for M. rosenbergii larvae was 27.1, with a 96 h-LOEC of 16.5, whereas the 96 h-LC₅₀ of carbonate alkalinity was 230.7 mg/L, with a 96 h-LOEC of 96.6 mg/L. Furthermore, salt-alkali interaction exhibited synergistic effects. Enzyme activity analysis revealed initial decreases followed by increases over time for alkaline phosphatase and Na⁺-K⁺-ATPase activities in the gills and hepatopancreas, whereas Ca²⁺-ATPase activity in the gills exhibited the opposite pattern. Superoxide dismutase activity in the hepatopancreas reached its lowest level during the mid-term stress period (72 h and 120 h), whereas catalase and glutathione S-transferase levels increased. Carbonic anhydrase activity showed an initial decrease followed by increase during the treatment process, with no significant differences observed among different saline-alkaline stress. Transcriptomic analysis revealed distinct responses of the gills and hepatopancreas to saline-alkaline stress. Up-regulated genes associated with extracellular space/region (e.g. tetraspanin), cellular response to xenobiotic stimulus (e.g. fatty aldehyde dehydrogenase), and secondary active transmembrane transporters were observed in the gills under saline-alkaline stress. Genes involved in the extracellular space/region were down-regulated in the hepatopancreas, whereas carbohydrate transmembrane transport related genes (e.g. lipocalin-like protein) were upregulated. These results suggest that M. rosenbergii adapts to saline-alkaline environments through coordinated osmotic regulation strategies, which include increased ion transport in the gills and enhanced carbohydrate transmembrane transport in the hepatopancreas. This study provides scientific evidence for understanding the adaptation mechanisms of M. rosenbergii in saline-alkaline environments.