Magnetic nanoparticles have attracted great attention and become promising candidates in the biomedicine field due to their special physicochemical properties. They are generally divided into metallic and non-metallic magnetic nanoparticles, according to their compositions. Both of the two types have shown practical values in biomedicine applications, such as drug delivery, biosensing, bioimaging, and so on. Research efforts are devoted to the improvement of synthesis strategies to achieve magnetic nanoparticles with controllable morphology, diverse composition, active surface, or multiple functions. Taking high repeatability, programmable operation, precise fluid control, and simple device into account, the microfluidics system can expand the production scale and develop magnetic nanoparticles with desired features. This review will first describe different classifications of promising magnetic nanoparticles, followed by the advancements in microfluidic synthesis and the latest biomedical applications of these magnetic nanoparticles. In addition, the challenges and prospects of magnetic nanoparticles in the biomedical field are also discussed.