Given the presence of emerging pollutants at low concentrations in water bodies, which are inevitably affected by background substances during the removal process. In this study, we synthesized molecularly imprinted catalysts (Cu/Ni-MOFs@MIP) based on bimetallic metal-organic frameworks for the targeted degradation of ciprofloxacin (CIP) in advanced oxidation processes (AOPs). The electrostatic interaction and functional group binding of CIP with specific recognition sites on Cu/Ni-MOFs@MIP produced excellent selective recognition (Qmax was 14.82 mg g−1), which enabled the active radicals to approach and remove the contaminants faster. Electron paramagnetic resonance (EPR) analysis and quenching experiments revealed the coexistence of ∙OH, SO42−, and 1O2, with ∙OH dominating the system. Based on experimental and theoretical calculations, the reaction sites of CIP were predicted and the possible degradation pathways and mechanisms of Cu/Ni-MOFs@MIP/PMS systems were proposed. This study opens up a new platform for the targeted removal of target pollutants in AOPs.