Magnetic-fluorescent composite nanoparticles as a new kind of nanoparticle have attracted much attention in recent years. The composite nanoparticles combine the fluorescent properties, magnetic properties and the physical properties of nano-size, so they can offer a range of potential applications, such as bioseparation and bio-imaging, tumor cell localization, and even cancer treatment. This Minireview will introduce the main synthesis strategies for the fabrication of magnetic-fluorescent composite nanoparticles, the current and potential bio-application of magnetic-fluorescent nanocomposites, including protein and DNA separation and detection, bio-imaging and sorting in vitro and in vivo, drug delivery and the cancer treatment.