Plant is the major source of active chemicals for human health. We developed an integrated research strategy to investigate the quality traits and the underlying molecular mechanism using Salvia miltiorrhiza as a model. Morphological traits were investigated by high-throughput image analysis. Accordingly, high-resolution metabolic analyses were performed to demonstrate the metabolic variation of active compounds and general metabolic flux. Subsequently, phenotypic and metabolic components were integrated for analyses of phenotypic variance, heritability, growth modeling, and traits correlation. Parameters generated by above analyses are promising for subsequent genetic mapping to uncover the genetic basis of quality traits by genome re-sequencing. The study strategy presented here will be useful to advance our views of medicine plants and key components underlying their quality traits. Meanwhile, it will provide opportunities to discover efficient genetic elements for metabolic engineering.