A large area of China is covered by saline-alkali water with high salinity, high pH, and ion ratio imbalance. Macrobrachium rosenbergii is an economically important aquaculture species worldwide due to its rapid growth and low demand for animal feed. Considering the fact that the M. rosenbergii has wide adaptability to salinity and high resistance to alkalinity stresses, an experiment was conducted to investigate the effects of carbonate alkalinity stress on the growth, reproduction, and intestinal health of M. rosenbergii to effectively utilize the abandoned saline-alkali water in China and establish a model of inland saline-alkali water cultured M. rosen­bergii. Juvenile M. rosenbergii [(2.85±0.12) g] were subjected to an acute carbonate alkalinity stress experiment to determine the 96-hour lethal concentration (LC₅₀). Based on this, four carbonate alkalinity concentrations, i.e., 1.5 (control group), 3, 6, and 9 mmol/L, designated as control C1, C3, C6, and C9, respectively, were used to culture triplicate groups for 56 d. The results showed that the 96-hour LC₅₀ value for juvenile M. rosenbergii under carbonate alkalinity stress was 17.955 mmol/L, with a safe concentration of 5.118 mmol/L. The survival, weight gain, and specific growth rates of juveniles decreased with increasing alkalinity concentrations, with significant reductions observed in the C9 group compared with the other experimental groups (P＜0.05). The feed conversion ratio in the C9 group was significantly higher than that in the other experimental groups (P＜0.05). Compared with the control group, carbonate alkalinity in the C6 and C9 groups significantly inhibited the spawning and egg incubation rates of adult prawns (P＜0.05). Transmission electron microscopy revealed that the structural integrity of the intestinal microvilli in juvenile prawns deteriorated with increasing carbonate alkalinity stress, with the most severe damage observed in the C9 group. Furthermore, the present study found that the intestinal peritrophic membrane structure of juvenile prawns was damaged by a higher concentration of carbonate alkalinity; and the peritrophic matrix structure of prawns in the C9 group using scanning electron microscopy technology showed increased damage and enlarged pore sizes under carbonate alkalinity stress. Alpha diversity analysis of the intestinal microbiota of juvenile prawns using Illumina MiSeq high-throughput sequencing showed that the flora richness index Chao1 in the C9 group had no significant diffrence from that of the control group (P＞0.05), but was significantly higher than that of C3 and C6 groups (P＜0.05). There was no significant difference in Shannon and Simpson intestinal flora diversity index among all experimental groups (P＞0.05). Proteobacteria, Bacteroidetes, Planctomycetes, Cyanobacteria, Actinobacteria, and Firmicutes dominated the bacterial communities of juvenile M. rosenbergii at the phylum level. At the genus level, the abundances of the pathogenic bacteria Flavobacterium and Pseudomonas in the C9 group were significantly higher than those in the control group (P＜0.05), suggesting that changes in the gut microbiota structure of juvenile M. rosenbergii exhibit an increased risk of disease outbreaks. These results suggested that chronic higher concentrations of carbonate alkalinity stress significantly affect the growth performance and reproductive and intestinal histology of juvenile prawns and disrupt the intestinal microbial community structure. Our study highlights that M. rosenbergii juveniles are suitable for large-scale saline-alkaline aquaculture in China.