Though well known for its anti-microbial property, copper is usually not considered for drinking water disinfection because of its health risk to human bodies under efficient biocidal concentration. Herein, we have rationally designed and constructed a tubular coaxial-electrode copper ionization cell (CECIC) that enables superior disinfection performance (~6-log removal of E. coli) with a very low effluent copper concentration (~200 μg/L). A non-uniform electric field with enhanced strength near the center electrode is generated in the chamber attributed to the coaxial center-outer electrode configuration. Exposure to the strong electric field subsequently increases the permeability of cell membrane, the excessive uptake of Cu ions into microbes, and thus the reinforced bacteria inactivation. The in-situ ionization results in a Cu ion concentration gradient with higher concentrations in the regions closer to the center. In addition, being driven by the electrophoresis and dielectrophoresis forces, the bacterial cells are transported to the vicinity of the center electrode, where both the electric field strength and Cu ion concentration are higher. These mechanisms in the CECIC synergistically result in the high inactivation efficiency with low Cu concentration in the effluent. The low-cost, high-efficiency, and disinfection-byproduct-free CECIC has shown significant potential in point-of-use applications.