Salvia miltiorrhiza is the source for the production of tanshinones and phenolic acids, which possess pharmacological properties for the treatment of cardiovascular and cerebrovascular diseases and hyperlipidemia. However, the biosynthetic mechanism of these bioactive secondary metabolites remains unclear. Transcriptome analysis is a promising tool to illustrate the biosynthesis, growth, and development of these bioactive compounds and the genetic diversity of S. miltiorrhiza. The next-generation sequencing (NGS) technologies, such as the second-generation sequencing (SGS) technologies (e.g., Illumina) and the third-generation sequencing technologies (e.g., PacBio), are suitable and widely used for transcriptome analysis of S. miltiorrhiza. NGS enables the identification of gene expression profiling and facilitates reliable discoveries of genes related to secondary metabolite biosynthetic pathway. At present, hybrid sequencing strategies integrating the strengths of SGS and PacBio sequencing have obtained considerable transcriptome information of medicinal plants. NGS provides useful information for the direct detection of genetic markers and alternative splicing events related to the biosynthesis of secondary metabolites that facilitate the rapid breeding of medicinal plants.