Studied with X-ray fluorescence spectrum analytic (XRF), powder X-ray diffraction (PXRD) and Fourier transform infrared spectroscopy (FTIR) for five different species of Salvia miltiorrhiza bge grew in Anguo, the intrinsic components and microstructures were determined and comprehensive characterization was carried out. The figure of comprehensive characterization can describe characteristics of intrinsic components from elements, crystal and amorphous active component, it can give an intuitive description for the same components and subtle differences in the intrinsic components of Salvia miltiorrhiza bge, which are different idioplasmatic and same species. It is the ideal method because of the simple preparation of sample, rapid and fine accurate measurement with reproducibility and objectivity, so that it can be used for breeding of fine varieties of Chinese medicinal materials, Chinese medicinal materials GAP guidance of growing conditions, medicinal origin characteristics, the intrinsic composition and microstructure characterization, quality control and authenticity of the identification.