Photocatalysis‐based advanced oxidation technologies have been developed as an attractive strategy for degrading pollutants. However, the question of how to increase removal specificity without sacrificing the degradation effect remains a difficult one. In this work, a photocatalytic system for the simultaneous targeted elimination of nine heterocyclic amines (HCAs) is established using a green‐prepared photocatalyst (CN@Mn–FeOOH@MIP) that activates sodium persulfate (PS) under visible light. Mn–FeOOH clusters are in situ covered on laminar g‐C3N4 (CN) carrier to form a heterojunction, along with a molecularly imprinted layer self‐polymerized from dopamine, which is grown on the outer layer, resulting in both the desired photochemical activity and specific sites for recognition. The conditions of composite and photocatalysis are explored and optimized for efficient and selective degradation. Notably, CN@Mn–FeOOH@MIP is synthesized free of any organic reagents, and the biosafety is confirmed by cellular and in vivo toxicity evaluation. The developed CN@Mn–FeOOH@MIP/PS system with visible‐light‐driven is applied to the removal of HCAs in coffee samples with the recoveries over 70% and the reuse rates greater than 85%. It coupled the advantages of specific enrichment and rapid degradation, which furnishes a novel approach for the control of trace thermal processing pollutants.