In the present study, an ultra performance liquid chromatography coupled with time-of-flight mass spectrometry (UPLC/Q-TOFMS) based on chemical profiling approach to evaluate chemical constitution between mixed decoction and co-decoction of monkshood-pinellia combination of the eighteen incompatible medications (Shi Ba Fan) was proposed.  Two different kinds of decoctions, namely monkshood-pinellia co-decoction: water extract of the two herbs together, and monkshood-pinellia mixed decoction: water extract of each individual herbs mixed together, were prepared.  Batches of these two kinds of decoction samples were subjected to UPLC/Q-TOFMS analysis, the datasets were processed with MassLynx 4.1 to holistically compare the difference between these two kinds of decoction samples.  The most changed components during decocting were analyzed.  Using the proposed approach, global chemical difference was found between co-decoction and mixed decoction, mesaconitine, aconitine and hypaconitine were identified as the most changed components (changed most significantly) during decocting.  Result shows significant difference between two kinds of decoction samples, and the significant differences are probably related to the incompatibility of monkshood and pinellia.