Magnetic nanospheres have numerous applications in biomedicine, biotechnology and wastewater treatment, due to their high surface area, tunable sphere size and superparamagnetic properties. Magnetic nanoparticles can be designed and endowed with optical, electronic and fluorescent properties, allowing a wide range of functionality. Multifunctional magnetic particles with heterodimer structures allow various kinds of target molecules to be attached onto their specific parts via affinity or coordinate bonding, etc. The abilities of these nanodevices, including the encapsulation of target molecules in magnetic hybrid nanostructures and easy magnetic separation in the presence of external magnetic fields, show much promise for magnetic imaging, magnetic separation and drug delivery. Consequently, magnetic particles offer excellent potential future uses in disease diagnosis, hyperthermia, immunoassays, electrochemical biosensors, contaminated water treatment and optical detection. In this article, we review the preparation and application of inorganic and organic magnetic composite spheres in the fields of magnetic separation, drug delivery, hyperthermia, magnetic resonance imaging, and others. The size, specific surface area, structure, magnetic properties and surface functional groups of nanospheres have a great influence on their effectiveness in these applications. The encapsulation of target molecules in magnetic hybrid nanostructures and their easy separation using an external magnetic field show promise for the fabrication of novel nanodevices for many applications.