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In the present study, a new strategy using UPLC-QTOF-MS based metabolomics coupled with diagnostic ion exploration for rapidly evaluating sulfur-fumigation caused holistic quality variation of medicinal herbs was proposed and validated by employing Moutan Cortex (MC) as an example.First, the UPLC-QTOF-MS data of MC and sulfur-fumigated MC (S-MC) were subjected to unsupervised segregation principal component analysis (PCA) and supervised orthogonal partial least squares discriminant analysis (OPLS-DA), three chemical markers in S-MC was found and elucidated to be pinane monoterpene glucosides sulfonates; Then, after exploring the MS fragmentation pattern of these chemical markers, a common sulfur-containing ion m/z 259 was selected as the diagnostic ion, and additional seven pinane monoterpene glucosides sulfonates were detected and identified in S-MS with the diagnostic ion extraction; Finally, the holistic quality variation of MC was further dissected by dynamic determination of these ten characteristic components at different durations of sulfur-fumigation.All the results indicated that sulfur-fumigation can induce chemical transformation of pinane monoterpene glucosides in MC, and the duration of sulfur-fumigation was a decisive factor in the holistic quality variation of S-MC, and that the proposed strategy should be applicable for rapid evaluation on sulfur-fumigation caused holistic quality variation of other medicinal herbs.