Abstract: Cotton is one of the most important economic crops in China, especially in Xinjiang. However, in the process of cotton production, it is often subject to salinity stress, which is an important environmental limiting factor, for the growth and development of cotton. A cotton cultivar named xinluzhong No. 69, with strong tolerance to salt stress, was screened from 4 main cotton cultivars in Xinjiang, to reveal the molecular mechanism of cotton salt tolerance. The results of transcriptome analysis showed that 891 genes were up-regulated and 666 genes were down-regulated in cotton roots. The results of GO enrichment analysis showed that the majority of differentially expressed genes were concentrated in molecular functions, cellular components and biological processes. KEGG analysis showed that the differentially expressed genes were mainly involved in lignin biosynthesis and plant MAPK signaling pathway.