To explore the differences in the gene expression of roots and leaves of Semiliquidambar cathayensis, and the expression rules of key genes in the biosynthesis of key active components of S. cathayensis. We carried out transcriptome sequencing and bioinformatics analysis for the roots and leaves of S. cathayensis. 59378 differentially expressed genes (DEGs) were classified into three major classes in GO classification, mainly involving biological process functions (50.59%). 626 DEGs were annotated in 24 categories of the KOG classification. A total of 81 differentially expressed genes involved in phenylpropane biosynthesis, 110 differentially expressed genes involved in flavonoid biosynthesis, and 211 differentially expressed genes involved in terpenoid biosynthesis. The transcriptomic data of roots and leaves of S. cathayensis were obtained, which laid a foundation for the study of functional identification, secondary metabolic pathway and regulation mechanism of S. cathayensis.