Background: In traditional Chinese medicine (TCM), raw and processed herbs are used to treat the different diseases. Fructus Arctii, the dried fruits of Arctium lappa l. (Compositae), is widely used in the TCM. Stir-frying is the most common processing method, which might modify the chemical compositions in Fructus Arctii. Materials and Methods: To test this hypothesis, we focused on analysis and identification of the main chemical constituents in raw and processed Fructus Arctii (PFA) by high-performance liquid chromatography/diode array detection-electrospray ionization-mass spectrometry. Results: The results indicated that there was less arctiin in stir-fried materials than in raw materials. however, there were higher levels of arctigenin in stir-fried materials than in raw materials. Conclusion: We suggest that arctiin reduced significantly following the thermal conversion of arctiin to arctigenin. In conclusion, this finding may shed some light on understanding the differences in the therapeutic values of raw versus PFA in TCM.