Photodisinfection by semiconductors has been proven to be an effective method for achieving antibacterial or antifungal activity. However, the toxicity of the nanomaterial to the environment and organisms is a major concern. Herein, a highly efficient and environmentally friendly photodisinfection material of a carbon dots (CDs) decorated Na2W4O13 composite with WO3 photocatalyst was fabricated via a facile hydrothermal-calcination approach. The TEM (transmission electron microscopy) images showed that CDs decorated the surface of the Na2W4O13 flakes. Compared with the samples without incorporated CDs, the as-synthesized composite of CDs/Na2W4O13/WO3 exhibited excellent antimicrobial activity against E. coli under visible light illumination. Electron spin resonance (ESR) spectroscopy and reactive species scavenging experiments revealed that the hydroxyl radicals and superoxide radical anions played the most important role in the photocatalytic bacterial inactivation. Furthermore, the cytotoxicity of the CDs/Na2W4O13/WO3 composite was evaluated by analyzing the viability of HepG2 and Chinese hamster lung (V79) cells using Cell Counting Kit-8 (CCK-8).