Halophyte plants could successfully survive in severe saline lands. However, the spatiotemporal responses of halophyte trees to salt stress are still largely unclear. Here, comprehensive transcriptome profiling analyses in the roots of T. chinensis tree in response to salt stress were conducted. After treatments with 300 mM NaCl for 12, 24 and 48 h, 4452, 4836 and 5222 differentially expressed genes (DEGs) were respectively identified. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that these DEGs identified at different treatment times were enriched in the same pathways. Further transcriptomic analyses demonstrated that gene encoding transcription factor genes, such as bHLH, Dof, MYB and NAC, and oxidative stress and sugar metabolism related genes, were differentially and time specifically expressed, especially at the time point of 12 h treatment. The results of this study will provide fundamental information for future study on the mechanism of halophyte plants in response to salt stress, and for the identification of new candidates genes usable for the molecular breeding of plant varieties with promoted tolerance to abiotic stress.