Although nanozymes exhibit properties superior to those of natural enzymes and conventional engineered enzymes, the development of highly specific nanozymes remains a challenge. New yolk-shell Fe3O4 molecularly imprinted (MIP@void@Fe3O4) nanozymes with peroxidase-like activity were developed by modelling the substrate channels of natural enzymes through molecular imprinting techniques and interfacial affinity modifications in this study. To establish a platform technology for the adsorption and determination of inorganic and organic contaminants, lead ion (Pb2+) and diazinon (DIZ), respectively, were selected as imprinting templates, and a hollow mesoporous shell was synthesized. The as-prepared MIP@void@Fe3O4 nanozymes, characterized using TEM, HRTEM, SEM, FT-IR, TGA, VSM and XPS, not only affirmed the successful fabrication of a magnetic nanoparticle with a unique hollow core-shell structure but also facilitated an exploration of the interfacial bonding mechanisms between Fe3O4 and other shell layers. The enrichment of the MIP@void@Fe3O4 nanozymes due to imprinting was approximately 5 times higher than the local substrate concentration and contributed to the increased activity. Based on selective and competitive recognition experiments, the synthesized nanozymes could selectively recognize organic and inorganic targets with the lowest detection limits (LOD) of 6.6 × 10-9 ppm for Pb2+ and 5.13 × 10-11 M for DIZ. Therefore, the proposed biosensor is expected to be a potent tool for trace pollutant detection, which provides a rational design for more advanced and subtle methods to bridge the activity gap between natural enzymes and nanozymes.