Based on Fourier transform infrared (FTIR) and Raman spectroscopy (FT - Raman), the effective medicinal composition and its content change of Qi chrysanthemum are directly and quickly determined among the virus-free breeding and sulfur smoked samples of three different groups. FTIR and FT-Raman spectra of three groups of Qi chrysanthemum sample are compared and analyzed. The results show that the intensities of multiple infrared absorption peaks are obvious different within the range of 1 800~500 cm-1 and the characteristic peak shapes are slightly different in the FTIR spectra of the three groups with obvious differences of characteristic peak shapes in FT - Raman spectrum have. FTIR and FT - Raman spectrum directly reflect that the stem tip virus-free breeding will make the volatile oil, flavonoids and other medicinal component content increase in Qi Chrysanthemum, but the sulfur smoked reduce. The FTIR, FT Raman spectroscopy for detection of effective medicinal composition changes in Qi Chrysanthemum caused by virus-free breeding or sulfur smoked establishes a scientific basis, also an effective method to test their component content.