In order to explore the effect of salinity stress on the intestinal gene expression level of Cherax quadricarinatus, Illumina Hiseq 2500 high-throughput sequencing platform was used to conduct bidirectional sequencing of intestinal tissues of C. quadricarinatus under different salinity conditions (0, 5, 10 and 15 psu). After quality control and assembly of the obtained raw data, 76 534 unigenes was obtained. Blast in NR, NT, KO, Swissprot, PFAM, GO and KOG databases, 37 378 unigenes could be annotated. The amount of gene expression was estimated according to FPKM (Fragments Per Kilo bases Per Million Fragments). Based on the protein annotation results of NR and Pfam databases, 448 362 unigenes were functional annotation. According to the relationship between KO functional annotation and Pathway, 9 483 unigenes were annotated and classified into 34 pathways. Gene expression differences were analyzed by DEGseq. 0 psu was used as the control group, and the screening conditions for significantly different genes were set as Q value<0.05 and multiple |Fold Change|>2. The 5, 10 and 15 psu groups obtained 2 733, 91 and 236 differentially expressed genes respectively, among which 2 068 genes were significantly up-regulated and 665 genes were significantly down-regulated, with the 5 psu group having the most differentially expressed genes. The KEGG pathway enrichment analysis of all differentially expressed genes showed that 5, 10 and 15 psu groups were enriched to 265, 80 and 120 pathways respectively, and only 10 psu and 15 psu groups had a significantly enriched pathway respectively, all of which were legionella pathways. After identification, legionella pathway was significantly down-regulated, which was consistent with the previous results of enterobacteriaceae. The results showed that red chelicerae could protect the intestinal tract from infection by exogenous pathogenic bacteria by inhibiting the relevant pathways and abundance of potential pathogenic bacteria under the condition of increased salinity. In addition, changing in differential genes (eEF1α, udp, UPP, ACTB_G1, TUBA，TUBB,PFN, CALM) suggest that increased salinity seriously affects the cellular morphology, intracellular material transport, and intracellular signal transduction in the gut of red chelicerae, and activates pyrimidine remediation pathways to repair genetic damage caused by uracil nucleotide imbalance. The results provide important reference materials for the saline-alkali or brackish aquaculture of C. quadricarinatus in the future, and provide reference for the further study of the intestinal immune regulation mechanism of C. quadricarinatus under salinity stress.