Salvia miltiorrhiza is a well-known medicinal plant and functional food in Asia. The range of quality among its germplasms is irregular, which inevitably affects its health and economic benefits. We established a system comprising phenotypic characteristics, ISSR markers, and active constituents to facilitate the comprehensive evaluation of this species. Concerning the phenotypic traits, 55 germplasms were characterized and divided into eight groups. ISSR molecular markers were employed to detect polymorphisms and distinguish germplasms by integrating with phenotypic characteristics. In terms of economic benefits, we were able to screen out the tall-stem and purple-stem types, both with good yields (root biomass) and high contents of active constituents, as members of a preferred-quality group in S. miltiorrhiza. Our study is the first to provide an overall assessment of different S. miltiorrhiza germplasms. The integrated investigation of the phenotypic, genetic, and phytochemical diversity of S. miltiorrhiza germplasms demonstrates the great potential of diverse genotypes to be exploited by plant breeders.