In order to evaluate chemical consistency between traditional and modern decoctions of Da-Cheng-Qi-Tang (DCQT), a classical Chinese medicine formula commonly used in the treatment of digestive diseases, an ultra performance liquid chromatography-electrospray ionization-quadrupole time-of-flight mass spectrometry (UPLC-ESI-Q-TOFMS) combined with multivariate statistical analysis was established to globally characterize the chemical profile and discover differentiating chemical markers. Two kinds of decoctions, namely traditional decoction (multi-step decoction of constituent herbs), and modern decoction (one-step decoction of all herbs), were prepared and subjected to UPLC-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 comprehensively compare the chemical difference between these two kinds of decoction samples. The global chemical difference was found between traditional and modern decoctions, and rhein, sennoside A/B, diosmetin, magnoloside B and naringin were the components contributing most to these differences. Based on the fact that traditional decoction of DCQT presents the higher concentration of rhein and sennoside A/B, mainly contributed to laxative activity of DCQT, the purgative effect of traditional decoction might be more potent, compared with modern decoction. However, the comparative study on purgative effect of traditional and modern DCQT remains to be further investigated using pharmacological approaches. Our findings also provide the early scientific evidence of traditional decoction method of DCQT.