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In the present study, an ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) based chemical profiling approach to rapidly evaluate chemical diversity after codecocting of the combination of Aconitum carmichaeli Debx. (wu-tou in Chinese, WT) and Bletilla striata (Thunb.) Reichb.f. (bai-ji in Chinese, BJ) incompatible pair. Two different kinds of decoctions, namely WT-BJ mixed decoction: mixed water extract of each individual herbs, and WT-BJ co-decoction: water extract of mixed two constituent herbs, were prepared. Batches of these two kinds of decoction samples were subjected to UPLC-QTOF/MS analysis, the datasets of tR-m/z pairs, ion intensities and sample codes were processed with supervised orthogonal partial least squared discriminant analysis (OPLS-DA) to holistically compare the difference between these two kinds of decoction samples. Once a clear classification trend was found in score plot, extended statistical analysis was performed to generate S-plot, in which the variables (tR-m/z pair) contributing most to the difference were clearly depicted as points at the two ends of “S”, and the components that correlate to these ions were regarded as the most changed components during co-decocting of the incompatible pair. The identities of the changed components can be identified by comparing the retention times and mass spectra with those of reference compounds and/or tentatively assigned by matching empirical molecular formulae with those of the known compounds published in the literatures. Using the proposed approach, global chemical difference was found between mixed decoction and co-decoction, and hypaconitine, mesaconitine, deoxyaconitine, aconitine, 10-OH-mesaconitine, 10-OH-aconitine and deoxyhypaconitine were identified as the most changed toxic components of the combination of WT-BJ incompatible pair during co-decocting. It is suggested that this newly established approach could be used to practically reveal the possible toxic components changed/increased of the herbal combination taboos, e.g. the Eighteen Incompatible Medications (Shi Ba Fan), in traditional Chinese medicines.