Identifying the alert groups of mechanism-based inactivators of human cytochrome P450s (hCYPs) is very helpful for early prediction of drug toxicity and for rational drug design to avoid idiosyncratic toxicity. Here, we report that a natural compound bufalin (BF) could time-dependently inactivate hCYP3A via complex CYP-catalyzed cascade oxidative metabolism. Metabolite profiling and time-dependent inhibition assays showed that 3-keto-bufalin (3-KBF), a unique nonpolar oxidative metabolite of BF, was the key substance responsible for hCYP3A inactivation. Further investigations demonstrated that 3-KBF was further metabolized by hCYPs to generate two mono-hydroxylated metabolites, which could be readily dehydrated and then covalently bound on glutathione or hCYP3A4. Collectively, this study uncovers unique CYP-catalyzed cascade oxidative pathways of BF in which two reactive intermediates bearing a Michael acceptor are finally formed as hCYP3A inactivators. These findings expand the current knowledge of CYP inactivators and suggest that some steroids bearing the 3-keto group may trigger time-dependent CYP3A inactivation.