Abstract: Transcriptome sequencing can be used for high-throughput sequencing of species under various environmental conditions. We explored the function and expression of related genes under specific conditions by gene structure analysis and gene function annotation. E. carinicauda samples at freshwater (salinity 0.2) and natural seawater (salinity 31) were sequenced by Illumina platform, and 13.92 Gb high-quality sequencing data was obtained. 111 618 transcripts and 72 734 unigenes were assembled. A total of 22 879 unigenes were annotated, of which 21 931 were compared to the Nr database. 1 492 differentially expressed genes were screened, including 829 up-regulated genes and 663 down-regulated genes, 810 of which were annotated. According to the GO function annotation, enrichment analysis and enrichment analysis of KEGG pathway of differentially expressed gene, we excavated differentially expressed genes of the natural seawater and freshwater environments, which provides technical support for further research on the physiological protection mechanism of E. carinicauda under low salinity stress.