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Atractylodis macrocephalae Rhizoma (AMR) is a famous classical Chinese traditional medicine (CTM), which has been used as a tonic for many diseases for thousands of years. In ancient China, it was used as a supplementary food for beauty in the palace. In preliminary studies, the function of whitening skin and the significant inhibiting effect on tyrosinase (TYR) which is the reactive enzyme in the composition of melanin of AMR were discovered, and the relevant research was rarely reported. In this study, high-performance liquid chromatography (HPLC) along with partial least squares regression analysis (PLS) was applied to survey the coherence between the chemical constituents and the inhibiting activity of 11 batches of AMR on TYR activity. The results of PLS showed that the chromatographic peaks 11 (atractylenolide III) and 15 could be important effective ingredients of the inhibition TYR activity as ascertained by spectrum-activity relationships. Furthermore, TYR inhibitory activity of atractylenolide III was validated by in vitro test by β-arbutin served as a positive control drug. The results of the in vitro test and the molecular docking showed that atractylenolide III has high TYR inhibitory activity and could link to the residues in TYR catalytic pocket. Therefore, bioassay, molecular docking, and spectrum-activity relationships are appropriate for linking the quality of samples with pharmaceutical-related active ingredients. And our studying would lay a theoretical foundation for applying the water extracts of AMR in whitening cosmetics.