MoS2-encapsulated hydrothermal carbonation carbon (HTCC@MoS2) heterojunction was constructed via a one-pot route. The HTCC@MoS2 nanospheres could efficiently inactivate 7-log bacterial cells within 50 min. Notably, as a metal-free material, pure HTCC nanostructures fabricated in this work also showed desirable photocatalytic activity. The continuously produced reactive species, especially % O-2 radicals, caused significant damage of bacterial cell membrane. The unique Z-scheme mode remarkably promoted the electron transfer and charge separation in the HTCC@MoS2 composite. This work not only developed a novel strategy for the direct conversion of carbohydrates to metal-free and photocatalytically active HTCC semiconductor, but also provided a promising HTCC@MoS2 heterojunction for cost-effective water disinfection.