Dioscorea bulbifera L. (DBL) is a common traditional Chinese medicine, with diosbulbin B (DSB) as its main toxic component. DSB-derived cis-enedial (DDE), an electrophilic intermediate produced during the metabolic activation of DSB, reacts with cysteine (Cys) and lysine (Lys) residues to form the corresponding pyrrole derivative in proteins. Cys-modified proteins were identified using tandem mass tagging-activity-based protein profiling (TMT-ABPP). The modification of hepatic acetyl-CoA acyltransferase 2 (ACAA2) was detected by TMT-ABPP, immunoprecipitation, and LC-MS/MS in mice treated with DSB or DBL, as well as in incubation of recombinant human ACAA2 with DDE. Molecular docking analysis further revealed that Cys128 and Lys143 likely participated in the formation of the pyrrole derivative. The protein adduction resulted in concentration- and dose-dependent inhibition of ACAA2 in vitro and in vivo. Accumulation of upstream triglycerides was observed in mice given higher doses of DSB, accompanied by a decrease of downstream acetyl coenzyme A levels, possibly resulting from the adduction of ACAA2.