Analytical methods based on ultraperformance liquid chromatography/ion-trap mass spectrometry (UPLC/ion-trap MS) were developed for quantification of atractylenolide I, II, and III in the methanol extract of Atractylodes japonica rhizomes with a C18 column in an acidified water/acetonitrile gradient eluent in an LC system, and ion-trap MS coupled with electrospray ionization was employed under positive-ion mode. The three atractylenolides were quantified in all A. japonica samples, and the content of atractylenolide I, II, and III showed a significant correlation to each other. Such high correlation was explained by the mechanistic insights into the biosynthetic pathway of atractylenoide III and I from atractylenoide II by using the biomimetic cytochrome P450 model, [Fe(tmp)](CF3SO3) (tmp = meso-tetramesitylporphyrin). Atractylenolides could be transformed by oxidation via the oxidative enzyme in the A. japonica plant. The present study first reports the first oxidative transformation of atractylenolides using the heme iron model complex.