In this paper, a new multiple -needle -cylinder reactor is designed to study the Escherichia coli inactivation with an unstable pulsed arc discharge in water and investigate the influence of several parameters for promoting its industrial application. The results show that the inactivation rate is mainly determined by energy density. About three orders reduction can be obtained with an initial cell count of 3 x 105 CFU/mL and energy density around 2 J/mL. The inactivation rate can almost reach 100% when the energy density is around 8 J/mL. For reaching the maximum inactivation rate of this system, the parameters including initial water conductivity below 50 itS/cm, initial cell count over 104 CFU/mL, and bubbling flow rate around 3.5 L/min are recommended. The water conductivity, pH value, and concentrations of hydrogen peroxide and ozone are also measured during the treatment to evaluate their influence. The transmission electron microscopy images of E. coli indicate that the intracellular morphology changes after plasma treatment.