Abstract The overlooked carbon source loss and uncontrolled CO 2 emission in water purification motivate the development of more sustainable catalytic systems. Herein, a charge‐asymmetric, metal‐free, dual‐functional‐site photocatalyst is designed by incorporating hydrogen‐affine fluorine onto nitrogen vacancy (Nv)‐rich graphitic carbon nitride (F‐CN‐Nv), enabling complete degradation and in‐situ upgrading of glyphosate (Gly) wastewater to CO (788 µmol g cat −1 h −1 ) with >99% selectivity. In‐situ spectroscopy and theoretical calculations uncover that the F‐species serve as a natural anchor toward ‐H 2 PO 3 group of Gly via hydrogen bonding interactions, which can purposefully adsorb Gly for C–P breaking, rendering exclusive CO formation. The synergistic interaction of Nv and F sites modulates the electronic configuration and surface polarization of F‐CN‐Nv to create a charge‐asymmetrical surface, enhancing the adsorption of O 2 at Nv. Additionally, the Nv‐mediated n‐π* electron transition accelerates the interfacial charge transfer and promotes the selective formation of •OH from O 2 through multi‐electron reduction, thereby improving the photocatalytic Gly degradation. Toxicity estimation software tool analysis reveals that the selective C─P bond cleavage of Gly by F‐CN‐Nv reduces the acute and developmental toxicity of Gly and its intermediates. This research recommends fully harnessing the redox potentials of photocatalysis for efficient purification and targeted upcycling of wastewater.