Biologically unsafe drinking water occurs in developing regions lack of centralized water treatment plants. Herein, Co3O4 nanowire electrodes with Co3O4 nanowire arrays grown on graphite felt were fabricated and employed to construct a flow-through electrode system (FES) for rapid and efficient water disinfection, which achieved over 6.7-log E. coli removal under applied voltage of 2.5 V and flow rate of 65 mL/min (HRT ∼ 4.5 s) with energy consumption of 2.3 Wh/m3. The FES also achieved over 6.7-log removal at 2.5 V for the Gram-negative P. aeruginosa under ∼ 60 mL/min and for Gram-positive bacteria (E. faecalis and S. aureus) under ∼ 40 mL/min, and the Gram-negative bacteria were more vulnerable to FES disinfection than Gram-positive ones due to their larger sizes and thinner cell walls. In-situ sampling and live/dead backlight staining experiments revealed that pathogen inactivation mainly occurred on anode via the sequential adsorption, inactivation and desorption processes under the mass transfer forces of electric field attraction and flow scouring effect in porous electrodes. The disinfection mechanisms on the Co3O4 nanowire anode were recognized to be electroporation and electrochemical oxidation, and the pores generated by electroporation can provide diffusion channels for reactive species into the pathogen cells, promoting the disinfection performance.