Abstract Bai-Zhu, the dried rhizome of Atractylodes macrocephala Koidz (AMK), is widely used as a tonic herbal in eastern Asia. It is commonly used as prepared slices in clinic by stir-frying with wheat bran (processed AMK). In the theories of traditional Chinese medicine (TCM), Bai-Zhu possesses significantly different therapeutic effects before and after processing. However, the molecular mechanics of this processing is still unknown. In this paper, the strategy of metabolomics was employed to investigate the changes of chemical constituents in Atractylodes macrocephala Koidz after processing. Meanwhile, the cell activity test variation of processed and unprocessed medicine was used to interpret the processing mechanism of AMK. Using ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC–QTOF/MS) with the method of multivariate statistic analyses including principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA), atractylenolide I, atractylenolide II, atractylenolide III, atractylenolide VI, 7-hydroxycoumarin, 8-β-methoxy atractylenolide I and Selina-4 (14), 7 (11)-dien-8-one were rapidly explored as the potential chemical markers of raw and processed AMK, respectively. Furthermore, it could be speculated that the processing mechanism of AMK was to increase the content of atractylenolide III which could strengthen the effect on gastrointestinal function.