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In this paper, boron-doped diamond (BDD) electro-activated persulfate was studied to decompose malachite green (MG). The degradation results indicate that the decolorization performance of MG for the BDD electro-activated persulfate (BDD-EAP) system is 3.37 times that of BDD electrochemical oxidation (BDD-EO) system, and BDD-EAP system also exhibited an enhanced total organic content (TOC) removal (2.2 times) compared with BDD-EO system. Besides, the degradation parameters such as persulfate concentration, current density, and pH were studied in detail. In a wider range of pH (2–10), the MG can be efficiently removed (>95%) in 0.02 M persulfate solution with a low current density of 1.7 mA/cm2 after 30 min. The BDD-EAP technology decomposes organic compounds without the diffusion limitation and avoids pH adjustment, which makes the EO treatment of organic wastewater more efficient and more economical.