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• The nanoreactor is obtained by the microwave-assisted surface imprinting technique. • Heterojunction formed between PEDOT and CdS improves the photocatalytic activity. • Fe 3 O 4 transfers photogenerated e- and further enhances the photocatalytic activity. • Imprinted cavity specifically adsorbs DM and improves the selectivity of nanoreactor. • PEDOT imprinted layer inhibites CdS photocorrosion and its secondary pollution. Magnetic imprinted PEDOT/CdS heterojunction photocatalytic nanoreactors are synergistically synthesized by the microwave-assisted surface imprinting technique. The coating of the PEDOT imprinted layer is conducive to the three-dimensional (3D) specific recognition and selective photocatalysis of danofloxacin mesylate due to the formation of imprinted cavities. The representative specific degradation selectivity coefficient of the developed nanoreactor relative to CdS/Fe 3 O 4 /HNT and magnetic non-imprinted PEDOT/CdS heterojunction is 2.08 and 2.11, respectively, clearly elaborating the excellent selectivity. The introduction of Fe 3 O 4 into PEDOT/CdS heterojunction enhances the transfer of photoexcited electrons, thereby, the photocatalytic activity has been significantly boosted up to ∼84.84 %. Meanwhile, the existence of PEDOT imprinted layer not only extracts the photoinduced holes produced by CdS, but also encapsulates CdS, which effectively inhibits the CdS photocorrosion and hinders its secondary pollution. With the improved selectivity and photocatalytic activity, our work paves the way to efficiently remove the target pollutant aiming at the practical application requirements. [ABSTRACT FROM AUTHOR]