A study was carried out on the disinfection efficiency of electrolyzed oxidizing water (EOW) on spores of Bacillus subtilis var. niger. The results showed a remarkable fungicidal rate of 100% after 20 min duration of 191mg/L active available chlorine (ACC). The disinfection effect was improved with increased ACC or prolonged disinfection time, while organic interferents exerted a strong concentration-dependent inhibition against the disinfection. The disinfection mechanism was also investigated at bio-molecular level. EOW decreased dehydrogenase activity, intensified membrane permeability, elevated suspension conductivity, and caused leakage of intracellular $K^+$, proteins, and DNA, indicating a damage of cell walls and membranes. Effects of EOW on microbiological ultra-structures were also verified by transmission electronic microscopy (TEM) images, showing that EOW destroyed protective barriers of the microbe and imposed some damages upon the nucleus area.