Na⁺/H⁺-exchanger is a membrane-associated enzyme responsible for the active transport of Na⁺ and H⁺ ions across cell membranes, and generates chemical and electrical gradients. It plays an important role in the aquatic adaptation of aquatic crustaceans. To investigate the function of the Na⁺/H⁺-exchanger in -exchanger 3 cDNA of (GenBank:MF373587), was cloned from the gill tissues of the animal by Reverse Transcription-Polymerase Chain Reaction (RACE). The full-length of cDNA was 3508 bp (base pairs), including a 2805 bp open reading frame (ORF) encoding a 934-amino acid peptide with one signal peptide and 12 transmembrane domains. Comparison with homologous proteins showed that the deduced Carcinus maenas (74%), and along with , were clustered into one group by phylogenetic analysis. Results of RT-qPCR showed that expression level in the gills was significantly higher than in other tissues ( in the gills was up-regulated under low pH stress (pH 5.2) during the entire duration of exposure. The expression level of in the gills was down-regulated during the first 48 h and up-regulated at 72 h under high pH stress (pH 9.1). After the knockdown of expression by RNA interference (RNAi), shrimp mortality was found to be significantly higher under low pH stress when compared with the control group. The results suggest that may play a more important role in regulating acid-base balance under low pH stress than under high pH stress.