The transcriptome represents the whole complement of RNA transcripts in cells or tissues and reflects the expressed genes at various life stages, tissue types, physiological states, and environmental conditions. Transcriptomics study concerning medicinal plants has become the most active area in medicinal plant genome research. Transcriptome analysis provides a comprehensive understanding of gene expression and its regulation. The study of its transcriptome has great significance in solving the questions of genetic evolution, genetic breeding, ecology and so on. Here we report the application status of transcriptomics in medicinal plants based on emergence, development and methodology of transcriptomics.