Metal-organic frameworks (MOFs) exhibit promising applications for the removal of organophosphorus pesticide contaminants. Herein, the magnetic CuFe2O4/MIL-101(Fe)(CFO/MIL) composite was prepared by a simple solvothermal method, which showed 95.0% degradation efficiency to organophosphorus pesticide chlorpyrifos (CP, 20.0 mg·L–1) after 60 min of simulated sunlight irradiation. When the illumination time was prolonged to 180 min, 97.5% of CP was effectively mineralized by CFO/MIL. After four cycles of magnetic recovery, the photocatalyst showed excellent stability and 75.7% CP removal efficiency. The adsorption performance of CFO/MIL on the PO43- further achieved the deep removal of organophosphorus pollutants. Based on the radicals scavenger experiment, the Z-scheme reaction mechanism was further proposed, which lead to faster charge transfer and higher photocatalytic activity. Moreover, the inhibition rate of Vibrio fischeri decreased to 23.0% after 180 min of illumination. Finally, the possible intermediates and degradation pathways of CP were speculated. Our work provides a new reference to construct highly efficient and easily recyclable MOFs photocatalysts for deep removal of organophosphorus pollutants.