Background: Sulfur-fumigation may induce chemical transformation of traditional Chinese medicines leading to harmful effects following patient ingestion. For quality control, it is urgently needed to develop a reliable and efficient method for sulfur-fumigation identification. Materials and Methods: The spectrochemical identification of non-fumigated and sulfur-fumigated Fritillaria thunbergii Miq. was carried out to evaluate inorganic elements and organic components. The concentrations of 12 elements, including Zn, Mn, Cu, Fe, Li, Mg, Sr, Pb, As, Cd, Hg, and S of samples were determined by microwave digestion - inductively coupled plasma atomic emission spectrometry (ICP-AES). Meanwhile, Fourier transform infrared spectrometry (FTIR) was used for the study of chemical group characteristic reactions after sulfur-fumigation. Results: The concentrations of Fe, Mg, Hg, and S elements showed significant differences between non-fumigated and sulfur-fumigated Fritillaria thunbergii Miq. The characteristic stretching vibrations of some groups in FTIR spectra, such as -OH, -S = O and -S-O, provided the identification basis for the discrimination of non-fumigated and sulfur-fumigated Fritillaria thunbergii Miq. Conclusion: The application of microwave digestion - ICP-AES was successfully used in combination with FTIR to authenticate and evaluate the quality of medicinal Fritillaria thunbergii Miq. Further applications of this technique should be explored.