The hypoxic microenvironment, continuous oxygen consumption, and poor excitation light penetration depth during antimicrobial photodynamic therapy (aPDT) tremendously hinder the effects on bacterial inactivation. Herein, a smart nanocomposite with oxygen‐self‐generation is presented for enhanced and selective antibacterial properties against anaerobe‐induced periodontal diseases. By encapsulating Fe3O4 nanoparticles, Chlorin e6 and Coumarin 6 in the amphiphilic silane, combined light (red and infrared) stimulated aPDT is realized due to the increased conjugate structure, the corresponding red‐shifted absorption, and the magnetic navigation performance. To address the hypoxic microenvironment problem, further modification of MnO2 nanolayer on the composites is carried out, and catalytical activity is involved for the decomposition of hydrogen peroxide produced in the metabolic processing, providing sufficient oxygen for aPDT in infection sites. Experiments in the cellular level and animal model proved that the rising oxygen content could effectively relieve the hypoxia in a periodontal pocket and enhance the ROS production, remarkably boosting aPDT efficacy. The increasing local level of oxygen also shows the selective inhibition of pathogenic and anaerobic bacteria, which determines the success of periodontitis treatment. Therefore, this finding is promising for combating anaerobic pathogens with enhanced and selective properties in periodontal diseases, even in other bacteria‐induced infections, for future clinical application.