A magnetic nanoaggregate-embedded bead (NAEB), a manufacturing method thereof and a bioparticle detection method using the same are disclosed. The magnetic NAEB has a protective nanoshell, noble metal nanoparticles, Raman reporter molecules and at least one magnetic nanoparticle. The protective nanoshell covers the noble metal nanoparticles, the Raman reporter molecules and the at least one magnetic nanoparticle. The noble metal nanoparticles, the Raman reporter molecules and the at least one magnetic nanoparticle form a magnetic nanoaggregate. Preferably, a chemical modification is performed on the magnetic NAEB, such that at least one targeting molecule is formed on an outer wall of the protective nanoshell, wherein a type of the targeting molecule is corresponding to a type of the bioparticle to be detected.
