In this article, palladium modification and silver modification were used as examples to demonstrate the disinfection effects on microorganisms in aqueous environment of photocatalytic transition-metal-ion-modified nitrogen-doped titanium oxide (TiON/M) materials. Transition metal ion modification was applied to TiON to take advantage of the coupling between transition metal ion addition and TiON semiconductor matrix under visible light illumination. The coupling promotes the separation of electron and hole pairs produced by photon excitation, thus it could reduce the intrinsic charge carrier recombination from anion-doping, which largely limits the photoactivity of TiON under visible light illumination. Large enhancements on the hydroxyl radical production and the photocatalytic disinfection efficiency on microorganisms under visible light illumination were observed for TiON with both palladium and silver modifications. The superior photocatalytic performance under visible light illumination suggests that the transition metal ion modification is an effective approach to reduce the massive charge carrier recombination from anion-doping and to enhance the photocatalytic performance of anion-doped TiO2. The resulting photocatalytic materials have the potential for a wide range of environmental applications.