Atomic level Ag loaded MnO2 porous hollow microspheres (Ag/MnO2 PHMs) were prepared by redox precipitation method, and utilized for E. coli inactivation under solar light irradiation. Ag nanoparticles (NPs) can be downsized into single atoms, thereby realizing highly utilization of Ag element as well as achieving superior photothermocatalytic E. coli inactivation for Ag/MnO2 than MnO2 PHMs. Under attack by the optimal 0.3%4/ MnO2 PHMs with atomic Ag, 7.11 logio cfu/mL cells can be completely inactivated within 10 min, much faster than the 0.3%Ag/MnO2 PHMs with Ag cluster (3.3 logio cfu/mL) prepared by photodeposition method, demonstrating the feasibility of redox precipitation to prepare efficient catalyst for water disinfection. Three effects are believed to contribute to this bacterial inactivation enhancement: (1) atomic Ag with high conductivity induces more formation of Mn3+ and oxygen vacancies in MnO2, which can efficiently accelerate the separation of hot electrons and holes generated by MnO2, collectively work with itself generated hot electrons to form into reactive species for photocatalysis; (2) atomic Ag exhibits strong local heating effect and induces higher reducibility for MnO2, considerably enhances the photothermal conversion and lattice oxygen activity of MnO2, thus promoting the thermocatalysis; and (3) the synergism of solar light driven photocatalysis and thermocatalysis through the activated OL. The highly efficient photothermocatalysis make the designed 3D atomic Ag/ MnO2 PHMs have a promising antibacterial ability for cleaning the microbial contaminated water environment.