This study presents a novel approach to enhance the performance of single-atom catalysts (SACs) for persistent Fenton-like reactions by embedding nitrogen vacancies (Nv) and iron (Fe) single-atom sites into g-C3N4. Through computational predictions and theoretical calculations, the optimal placement of Nv and Fe sites was identified, leading to a significant enhancement in visible-light absorption and charge transfer dynamics. The integration of Nv into the catalyst design increased electron density around Fe atoms, resulting in a potent and flexible photoactivator for peracetic acid (PAA). The catalyst demonstrated remarkable stability and effectively degraded various organic contaminants over 20 cycles with self-cleaning properties. The Nv sites captured electrons, enabling their swift transfer to adjacent Fe sites under visible light irradiation, which accelerated the reduction of the "peracetic acid-catalyst" intermediate. Theoretical calculations elucidated the synergistic interplay of dual mechanisms, highlighting increased adsorption and activation of reactive molecules. Electron reduction pathways on the conduction band were explored, revealing the production of reactive species that enhanced photocatalytic processes. A six-flux model was applied to optimize the photocatalytic process, providing insights for future photocatalyst design. The study offers a molecule-level insight into the rational design of robust SACs in a photo-Fenton-like system, with promising implications for wastewater treatment and other high-value applications. The system demonstrated efficient degradation of bisphenol A (BPA) under visible light, achieving complete removal and 63.1% mineralization. The catalyst's stability was confirmed over 20 cycles, and it showed self-cleaning properties. The study also explored the role of Nv and Fe sites in molecular activation, revealing their synergistic effects in enhancing catalytic activity. The results highlight the potential of Nv-rich Fe SACs for efficient and sustainable photocatalytic processes.This study presents a novel approach to enhance the performance of single-atom catalysts (SACs) for persistent Fenton-like reactions by embedding nitrogen vacancies (Nv) and iron (Fe) single-atom sites into g-C3N4. Through computational predictions and theoretical calculations, the optimal placement of Nv and Fe sites was identified, leading to a significant enhancement in visible-light absorption and charge transfer dynamics. The integration of Nv into the catalyst design increased electron density around Fe atoms, resulting in a potent and flexible photoactivator for peracetic acid (PAA). The catalyst demonstrated remarkable stability and effectively degraded various organic contaminants over 20 cycles with self-cleaning properties. The Nv sites captured electrons, enabling their swift transfer to adjacent Fe sites under visible light irradiation, which accelerated the reduction of the "peracetic acid-catalyst" intermediate. Theoretical calculations elucidated the synergistic interplay of dual mechanisms, highlighting increased adsorption and activation of reactive molecules. Electron reduction pathways on the conduction band were explored, revealing the production of reactive species that enhanced photocatalytic processes. A six-flux model was applied to optimize the photocatalytic process, providing insights for future photocatalyst design. The study offers a molecule-level insight into the rational design of robust SACs in a photo-Fenton-like system, with promising implications for wastewater treatment and other high-value applications. The system demonstrated efficient degradation of bisphenol A (BPA) under visible light, achieving complete removal and 63.1% mineralization. The catalyst's stability was confirmed over 20 cycles, and it showed self-cleaning properties. The study also explored the role of Nv and Fe sites in molecular activation, revealing their synergistic effects in enhancing catalytic activity. The results highlight the potential of Nv-rich Fe SACs for efficient and sustainable photocatalytic processes.