Developing highly active photocatalysts towards effective microorganism inactivation is a green and energy-smart strategy in response to the growing demands to water quality under the background of the water crisis. Here, a vertical face-to-face heterojunction is fabricated by horizontally assembling TiO2 nanosheets with {001} facets exposed on graphitic carbon nitride (g-C3N4) sheets through a facile hydrothermal driving coupling. The vertical heterojunction could almost completely disinfect 103 CFU/mL E. coli within 30 min under solar light, which is more efficient than the physically mixed composite and pure g-C3N4 and TiO2. The two-dimensional (2D) morphology provides ample surface area in forming the vertical heterojunction and enables intimate contact which is advantageous to charge transfer between g-C3N4 and TiO2. A Z-scheme charge transportation mechanism is confirmed through band structure analysis and reactive species (RSs) probing and trapping experiments. In comparison with physically mixed composite and the single-phase counterparts, the nanocomposite based on a Z-scheme electron transfer mode effectively prompts charge pair dissociation and subsequently encourages bacterial inactivation by boosting the generation of RSs. The constructing vertical Z-scheme heterojunction highlights the potential of 2D nanomaterials for accelerated water sterilization.