Carbon-defect engineering in single-atom metal-nitrogen-carbon (M─N─C) catalysts by straightforward and robust strategy, enhancing their catalytic activity for volatile organic compounds, and uncovering the carbon vacancy-catalytic activity relationship are meaningful but challenging. In this study, an iron-nitrogen-carbon (Fe─N─C) catalyst is intentionally designed through a carbon-thermal-diffusion strategy, exposing extensively the carbon-defective Fe─N4 sites within a micro-mesoporous carbon matrix. The optimization of Fe─N4 sites results in exceptional catalytic ozonation efficiency, surpassing that of intact Fe─N4 sites and commercial MnO2 by 10 and 312 times, respectively. Theoretical calculations and experimental data demonstrated that carbon-defect engineering induces selective cleavage of C─N bond neighboring the Fe─N4 motif. This induces an increase in non-uniform charges and Fermi density, leading to elevated energy levels at the center of Fe d-band. Compared to the intact atomic configuration, carbon-defective Fe─N4 site is more activated to strengthen the interaction with O3 and weaken the O─O bond, thereby reducing the barriers for highly active surface atomic oxygen (*O/*OO), ultimately achieving efficient oxidation of CH3SH and its intermediates. This research not only offers a viable approach to enhance the catalytic ozonation activity of M─N─C but also advances the fundamental comprehension of how periphery carbon environment influences the characteristics and efficacy of M─N4 sites.