Remarkable enhancement in degradation effect is achieved at in situ activated boron-doped diamond (BDD) and Pt anodes with different extent through electrochemical oxidation (EC) of 2,4-dichlorophenoxyacetic acid (2,4-D) with microwave (MW) radiation in a flow system. Results show that when EC is activated with MW radiation, the complete mineralization time of 2,4-D at the BDD is reduced quickly from 10 to 4 h while Chemical oxygen demand (COD) removal at Pt is increased from 37.7 to 58.3% at 10 h; the initial current efficiency is both improved about 1.5 times while the pseudo-first-order rate constant is increased by 153 and 119% at the BDD and Pt, respectively. To gain insight into the higher efficiency in microwave activated EC, the mechanism has therefore been systematically evaluated from the essence of electrochemical reaction and the accumulated hydroxyl radical concentration. 2,4-Dichlorophenol, catechol, benquinone, and maleic and oxalic acids are the main intermediates on the Pt anode measured by high performance liquid chromatography (HPLC), while the intermediates on the BDD electrode include 2,4-dichlorophenol, hydroquinone, and maleic and oxalic acids. The reaction pathway with microwave radiation is the same as that in a conventional electrochemical oxidation on both electrodes. While less and lower aromatic intermediates produce at the BDD with MW, which suggests the higher ring-open ratio and the faster oxidation of carboxylic acids. With microwave radiation, the ring-open ratio at the BDD is increased to 98.8% from 85.6%; the value at Pt is increased to 67.3% from 35.9%. So microwave radiation can activate the electrochemical oxidation, which leads to the higher efficiency. This promotion is mainly due to the higher accumulated hydroxyl radical concentration and the effects by microwave radiation. All the results prove that the BDD electrode presents much better mineralization performance with MW. To the best of our knowledge, it is the first time the systematic analysis of the mechanism of microwave activated EC has been reported.