Biohazards are widely present in wastewater, and contaminated water can arouse various waterborne diseases. Therefore, effective removal of biohazards from water is a worldwide necessity. In this study, a novel all-solid-state Z-scheme g-C3N4/m-Bi2O4 heterojunction was constructed using a facile hydrothermal approach. Using the optimum g-C3N4/m-Bi2O4 (1:0.5), 6 log10 cfu/mL of E. coli K-12 could be completely inactivated within 1.5 h under visible light irradiation, while only 1.2 log10 cfu/mL and 3.2 log10 of E. coli K-12 were inactivated by pure g-C3N4 and Bi2O4 under the same experimental conditions respectively. Emphasis was placed on identifying how the charge transfers across the g-C3N4/m-Bi2O4 heterojunction and a Z-scheme charge transfer mechanism was verified by reactive species trapping and quantification experiments. The Z-scheme charge separation within g-C3N4/m-Bi2O4 populated electrons and holes into the increased energy levels, thereby enabling one-step reduction of O2 to H2O2 and facilitating more generation of holes. This greatly accelerated photocatalytic efficiency on the inactivation of E. coli. Moreover, microscopy images indicate that cell structures were damaged and intracellular components were leaked out during the photocatalytic inactivation process. This study suggests that the newly fabricated Z-scheme g-C3N4/m-Bi2O4 is a promising photocatalyst for water disinfection.