Decoction, the characteristic heat-treatment procedure in Zhenjiang Aromatic Vinegar (ZAV) processing, was performed in laboratory to investigate its effect on the antioxidative activity (AA) of ZAV. Owing to the laboratory-scale decoction, DPPH radical scavenging activity, ORAC value and cellular antioxidant activity (CAA) of ZAV increased by 63, 24 and 54% of that of undecocted vinegar, respectively. Enzymatic assay and HPLC determination proved that phenolic content decreased after the decoction, while melanoidins, also with antioxidative activity and recently found in ZAV, were generated. Regardless of the fluctuation in AA of melanoidins during decoction, increased melanoidin content was responsible for the increase in AA of ZAV. At the end of the decoction, melanoidins accounted for 57.1 and 44.1% of the total AA of ZAV, according to DPPH and ORAC assay, respectively. Incorporation of phenolic compounds into melanoidins and degradation of melanoidins might both occur during decoction.