Here, we present a strategy to fabricate multifunctional polystyrene (PS) microbeads with carboxyl ends which exhibit magnetism and fluorescence. The strategy includes two steps: the preparation of porous PS microbeads with carboxyl-ends by combination of dispersion polymerization and seeded polymerization. and the facile process of embedding quantum dots (QDs) and magnetic nanoparticles (MNPs) into microbeads. The results indicate that the multifunctional PS microbeads (MFMs) can be dispersed in water stably and are well suitable for target encoding, capturing, and enrichment.