Extensive genomic data concerning medicinal plants are rather scarce and insights of the secondary metabolic pathways and their regulatory mechanism are insufficient, hampering the broad application of cell or tissue cultivation and metabolic engineering to producing high-value secondary metabolites. The integration of cDNA-AFLP based transcript profiling and metabolomics, a new development of functional genomic approaches could establish correlations between the changes of secondary metabolites and expressions of related genes. It has manifested widely applicative prospects in seeking genes involved in biosynthesis of secondary metabolites and exploring secondary metabolic pathways. Functional genomic approaches are promising trends in the field of medicinal plants secondary metabolites research and will lead to better utilization of natural medicinal resources.