In this study, two types of Danshen from different growth years were discriminated and identified by a three-step infrared spectroscopy method (Fourier transform-infrared spectroscopy (FT-IR) coupled with second derivative infrared spectroscopy (SD-IR) and two dimensional correlation infrared spectroscopy (2D-IR)). Though only small differences were found in the FT-IR spectra of the samples, the positions and intensities of peaks at around 1635 and 1055 cm⁻¹ could be considered as the key factors to discriminate them. More significant differences were exhibited in their SD-IR spectra, particularly the significant absorption bands attributed to polysaccharides and phenolic acids. The visual 2D-IR spectra provided dynamic chemical structure information of Danshen samples, which present different particular auto peak clusters in the range of 1000–1160 cm⁻¹ and 1430–1700 cm⁻¹, respectively. Furthermore, twenty different samples including ten of each herb were also successfully classified by soft independent modeling of class analogy (SIMCA). This study offers a promising method inherent with cost and time savings to characterize and control the quality of extremely similar and complicated herbal medicines like Danshen.