Electrocatalytic hydrodehalogenation (ECHD) offers a promising approach for detoxification of the halogenated antibiotics via hydrogenolysis of the C-X bonds (X = F, Cl or Br). Herein we demonstrated that the commercially-available cobalt phthalocyanine (CoPc) molecules with a high-loading of −[Co-N4]- moieties (Co wt%: 10.8 %) were exceptionally active for hydrogenolysis of the C-Cl bonds in florfenicol (FLO). It afforded an impressive mass activity of 6.2 gFLO h−1 g-1Co, a low Co leaching of 0.34 μg/L and a strong tolerance to interference from impurities in water, significantly surpassing reported Co/Fe/Ni-based particle and single-site counterparts. Mechanistic studies revealed that the ECHD on CoPc underwent a direct electron transfer manner rather than the atomic hydrogen (H*)-mediated indirect way, and the ECHD efficacy was affected by both the electron and proton transfer kinetics. The single-atom Co, with its d orbitals constituting the lowest unoccupied molecular orbitals of CoPc, served as the primary active site. It facilitated both electron and proton transfer, as well as the cleavage of the C-Cl bond but not the C-F bond. In a continuous-flow cell, the CoPc/C-driven ECHD reduced the antibacterial activity of a FLO-contaminated natural lake water sample by 90.8 % with an energy consumption of 0.19 kwh g-1FLO. This study highlighted great promise of the single-atom metal-bearing molecular catalyst toward the sustainable detoxification of halogenated antibiotics-contaminated water.