Single-atom photo-Fenton (PF) reaction is widely employed for the degradation of antibiotics and water disinfection. However, the key fundamental issues of the valence state cycling of single-atom metals and the activation of hydrogen peroxide (H2O2) in the PF process remain indistinct. Herein, we developed a catalyst donated as Cu single atoms anchored hydrangea-like carbon nitride (Cu-SA/CNH) with Cu−N4 coordination for PF reaction. Compared to pristine CNH, the Cu-SA/CNH exhibited a 2.42-fold increase in PF kinetics. The Cu-SA/CNH/PF system achieved 98.1% degradation efficiency of tetracycline and effectively inactivated Escherichia coli within 30 min. Density functional theory calculations demonstrated that the formation of Cu−N4 effectively improved the energy of the Cu d orbitals, leading to the generation of intermediate states that facilitated the Cu2+/Cu+ cycle. The adsorption capacity of Cu dxz orbitals on H2O2 increased nearly 10 times. This work provides valuable insights for enhancing single-atom PF activity to address environmental pollution.