Purple (Pr) mutant cauliflower has a bright color and high nutritional value. During postharvest storage, purple cauliflower fades in color and gradually develops a pungent flavor, which directly affects its commercial value. In this study, six anthocyanin-related metabolites were identified in postharvest Pr mutants via metabolomic analyses. Gene–metabolite association analysis revealed that 6-gingerol was the main component responsible for the pungent flavor of the Pr mutant, and that this compound was a component of the stilbenoid, diarylheptanoid, and gingerol biosynthesis pathways. The pungent flavor was correlated with the expression level of caffeoyl coenzyme A O-methyltransferase (CCoAOMT). In vitro experiments confirmed that the transcription factor (TF) BoMYB2 specifically binds to the BoCCoAOMT promoter through the MBS site. Additionally, transient expression analysis confirmed that BoMYB2 negatively regulates BoCCoAOMT transcription and promotes 6-gingerol accumulation, thereby influencing flavor formation in the Pr mutant. Our findings reveal the key genes and TF for the flavor-related transcriptional regulatory mechanism of postharvest Pr mutant cauliflower, and provide a valuable basis for developing postharvest preservation technology for commercial crops.