Abstract: The amount of sulfur dioxide residue is currently employed by Chinese Pharmacopoeia (CP) as an index to screen sulfur-fumigated herbs, but it is unclear if this index can objectively reflect the quality of sulfur-fumigated herbs. In the present study, sulfur-containing derivatives were confirmed in sulfur-fumigated Moutan Cortex (MC) by UPLC-QTOF-MS/MS analysis, and the contents of sulfur-containing derivatives and sulfur dioxide residues were statistically analyzed both in self-made and commercially available sulfur-fumigated and non-fumigated MC as well as the samples thereof before and after eight-month storage. The amount of sulfur dioxide was significantly decreased, but that of the newly-generated sulfur-containing markers was not, after eight-month storage of the sulfur-fumigated MC samples, indicating that the amount of sulfur dioxide residue may not be positively correlated with the quality of sulfur-fumigated MC. Therefore, sulfur dioxide residue index alone may not objectively reflect the sulfur-fumigation extent (quality change extent) of MC, more specific method using characteristic sulfur-containing derivatives as chemical markers should be developed to supplement the sulfur dioxide residue determination in the quality control of sulfur-fumigated MC.