A flow-through electro-peroxone system (E-peroxone) consisting of electrolysis and ozonation was developed for the disinfection of two kinds of simulated ballast water. This technology fulfilled the efficient generation center dot OH by reaction of ozone with the in-situ electrochemical production of H2O2, showing one order of magnitude higher inactivation of Escherichia coli (E. coli) than ozonation and electrolysis. Several experimental factors were optimized, such as aeration rate, current and flow rate. The concentration of hydroxyl radical and free chlorine was measured to be 14.7 mu M and 3.2 mg/L at the current of 50 mA, aeration rate of 50 mL/min and flow rate of 7 mL/min. The free chlorine did not play a main role in the disinfection in the E-peroxone process. The inactivation efficiency log(c/c(0)) reached -5.5 when the initial concentration of E. coli was 10(6) - 10(7) CFU/mL in the influent and the disinfection effect could last for five days. At initial E. coli of 0.6 x 10(4) CFU/mL, the effluent could meet the D-2 standard proposed by International Maritime Organization (IMO). Furthermore, the energy consumption of the E-peroxone system for treating these two solutions was 0.33 and 0.12 kW h/m(3), respectively. Moreover, the trihalomethanes (THMs), one of disinfection by-products (DBPs), could meet the WHO's (World Health Organization) drinking water standard. Therefore, the flow-through E-peroxone system was cost-effective and promising for the disinfection of simulated ballast water.