Backgrounds and aims Sweet sorghum is an annual C4 crop with a high salt tolerance. However, little is known about the molecular mechanisms of salt exclusion in roots of sweet sorghum. In this study, the physiological parameters and transcript profiles of two inbred lines of sweet sorghum roots (salt-tolerant M-81E and salt-sensitive Roma) were analyzed in the presence of 0 or 150 mM NaCl in order to elucidate the molecular mechanisms of salt exclusion. Results We found that the Na+ concentrations in both shoots and roots of M-81E were lower than that of Roma. Moreover, we identified 2085 and 3172 differentially expressed genes between control plants and those subjected to salt stress in M-81E and Roma strains, respectively. The differentially expressed genes involved in pathways related to salt exclusion such as formation of root casparian bands and suberin lamellae, membrane-bound ion translocating proteins. Many of these genes underwent greater change in M-81E compared to Roma. These results revealed that the better ability of salt exclusion in M-81E may be caused by the combination of physical barrier effect of root apoplastic barriers and the transportation of Na+ out of the xylem by HKT1;5. Moreover, some genes encoding transcription factors were also differentially expressed, which may be involved in the regulation of genes related to salt exclusion. Conclusions This RNA-seq dataset provide comprehensive insights into the transcriptomic landscape to reveal molecular mechanisms of salt exclusion in roots of sweet sorghum.