Comprehensive SummaryThe control of protein functions with light is valuable for spatiotemporal probing of biological systems. Current small‐molecule photo‐ modulation methods include the light‐induced uncaging of inhibitors and chromophore‐assisted light inactivation with reactive oxygen species (ROS). However, the constant target protein expression results in inadequate photo‐modulation efficiency, particularly for less potent inhibitors and chromophores. Herein, we report a novel bifunctional small‐molecule ligands strategy to photo‐modulate gene‐editing enzymes CRISPR/Cas9. A coumarin‐derived small‐molecule ligand Bhc‐BRD0539 is developed to uncage the active inhibitor upon light irradiation and to generate ROS in the Cas9 proximity for the dual inhibition of Cas9 activity. Our results highlight the synergistic photo‐modulation with bifunctional small‐molecule ligands, which offers a valuable addition to current CRISPR/Cas9 photo‐modulation technologies and may extend to other protein classes.