A magnetic molecularly imprinted polymer-based fluorescent (MIP-FL) probe has been synthesized by embedding glutathione-stabilized gold nanoclusters (GSH-AuNCs) and Fe3O4 nanoparticles (Fe3O4NPs) into silica composites. The Fe3O4NPs/AuNCs@MIPs are characterized by scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, and UV?Vis absorption spectroscopy. The results show that the spherical Fe3O4NPs/AuNCs@MIPs contain a core-shell structure with GSH-AuNCs anchored on the surface of silica-protected Fe3O4NPs. As a fluorescence probe (excitation: 360?nm, emission: 615?nm), Fe3O4NPs/AuNCs@MIPs can selectively detect metronidazole (MNZ) among other nitroimidazoles (ronidazole, ornidazole, and tinidazole). During the detection, the fluorescence intensity of the MIP-FL probe drops gradually with increasing MNZ concentration. The sensitive linear range of the fluorescence probe is from 0 to 5 ?M, and the limit of detection is 4.2 nM. After the recognition sites interact with the template, the occurrence of charge transfer from the GSH-AuNCs to MNZ results in fluorescence quenching. Finally, a real sample test has been performed in spiked milk. Satisfactory recoveries spanning from 96% to 102% indicate that Fe3O4NPs/AuNCs@MIPs enable highly sensitive detection of MNZ based on fluorescence signal output, while the MIPs also have enrichment potential for the target from complex samples due to the magnetic properties.