Antibiotics and antibiotic resistance genes (ARGs) are still a problem in biological treatment. Herein, we propose a synergetic strategy between microbes and dual-electric centers catalysts (CCN/Cu-Al2O3/ceramsite) for Ciprofloxacin (CIP)-contained (5 mg/L) water treatment in an up-flow biological filter. CIP was cleaved into small molecules by the catalyst, bringing a 57.6% removal and reducing 10.5% ARG. The characterization results verified that a Cu-π electrostatic force occurs on the catalyst surface, forming electron-rich areas around Cu and electron-poor areas at the carbon-doped g-C3N4 (CCN) aromatic ring. Thus, the electrons of adsorbed CIP were delocalized and then captured by the adsorbed extracellular polymeric substance at the electron-rich areas. Therefore, the synergetic process weakened the stress of CIP on bacteria and reduced ARG accumulation. It also enriched more electro-active bacteria on the surface of CCN/Cu-Al2O3/ceramsite, promoting the expression of extracellular electron transfer-related genes and reconstructing the energy metabolism mode. This result provides an opportunity for refractory antibiotic treatment in the biological process.