Salinity is one of the major environmental factors that limit the growth and development of plants worldwide. It has been documented that Na⁺/H⁺ transporters play a crucial role in salt tolerance and the development of plants. In this study, the genome-wide of NHX genes of Casuarina equisetifolia L. were identified and analyzed by bioinformatics method, and the expression of NHX genes in C. equisetifolia under salt stress was detected by qRT-PCR for exploring the biological function of CeqNHX gene family, which laid a theoretical foundation for further research on salt stress mechanism and digging out its resistance genes. The results were summarized as follows: (1) eight CeqNHXs (CeqNHX1-8) were identified, and phylogenetic analyses showed that they belong to three subfamilies (Endo, Vac, and PM), containing 1, 5, and 2 genes, respectively; the number of coding amino acids were 324-546, and the molecular weight were 34.87-60.27 kD, the theoretical isoelectric points were between 6.29-9.08, all of which were hydrophobic amino acids. (2) Gene structure and motif analysis revealed that the number of exons range from 2 to 17, and all contain Na⁺/H⁺ exchange conserved domains; the secondary structure were mainly composed of α-helix and random coil. (3) The promoter regions of CeqNHX genes contain a large number of abiotic stress and hormone response elements, among which, the CeqNHX5 promoter contains 13 kinds and 38 elements. (4) The results of qRT-PCR showed that the CeqNHX genes were expressed differently in different tissues, and most members were mainly expressed in shoots. Under NaCl stress condition, the expression of 8 CeqNHXs in C. equisetifolia was up-regulated to a certain extent. Studies had shown that CeqNHX genes might be involved in the regulation of various hormones and stress responses, and the expression of CeqNHXs was significantly responsive to salt stress, suggesting that CeqNHXs might be related to salt tolerance of C. equisetifolia.