[Objective] Through sequencing and genetic function analysis of the transcripts of Dunaliella salina, we studied its response to salt stress. [Methods] The transcriptome of Dunaliella salina under 9% and 24% NaCl concentration was obtained and sequenced by Illumina platform. All the unigenes were finally obtained by sequence splicing, redundancy removing based on the sequence clustering software. Functional notation and cluster analysis of unigenes were performed by comparing the unigenes to the database. [Results] A total of 40682 unigenes were obtained, including 10905 in the NR database, 2768 in the NT database, 7261 in the Swiss-prot database, and 6499 in the COG/KOG database. By comparing cells grown under hyper-and hyposaline conditions, 717 genes (41.46%) increased expression and 1012 genes (58.5%) decreased expression. Through the data integration analysis, 60 different expression genes of Dunaliella salina under salt stress were excavated. [Conclusion] Salinity stress up-regulated key genes in photosynthesis. Our findings provide reference for dissecting molecular mechanisms of salinity tolerance in algae and higher plants.