Traditional surgical intervention and antibiotic treatment are poor and even invalid for chronic diseases including periodontitis induced by diverse oral pathogens, which often causes progressive destruction of tissues, even tooth loss, and systemic diseases. Herein, an ointment comprising atomic-layer Fe2O3-modified two-dimensional porphyrinic metal-organic framework (2D MOF) nanosheets is designed by incorporating a polyethylene glycol matrix. After the atomic layer deposition surface engineering, the enhanced photocatalytic activity of the 2D MOF heterointerface results from lower adsorption energy and more charge transfer amounts due to the synergistic effect of metal-linker bridging units, abundant active sites, and an excellent light-harvesting network. This biocompatible and biodegradable 2D MOF-based heterostructure exhibits broad-spectrum antimicrobial activity (99.87 ± 0.09%, 99.57 ± 0.21%, and 99.03 ± 0.24%) against diverse oral pathogens (Porphyromonas gingivalis, Fusobacterium nucleatum, and Staphylococcus aureus) by the synergistic effect of reactive oxygen species and released ions. This photodynamic ion therapy exhibits a superior therapeutic effect to the reported clinical periodontitis treatment owing to rapid antibacterial activity, alleviative inflammation, and improved angiogenesis.