With unique physicochemical properties and biological effects, magnetic nanomaterials (MNMs) play a crucial role in the biomedical field. In particular, magnetic iron oxide nanoparticles (MIONPs) are approved by the United States Food and Drug Administration (FDA) for clinical applications at present due to their low toxicity, biocompatibility, and biodegradability. Despite the unarguable effectiveness, massive space for improving such materials’ performance still needs to be filled. Recently, many efforts have been devoted to improving the preparation methods based on the materials’ biosafety. Besides, researchers have successfully regulated the performance of magnetic nanoparticles (MNPs) by changing their sizes, morphologies, compositions; or by aggregating as-synthesized MNPs in an orderly arrangement to meet various clinical requirements. The rise of cloud computing and artificial intelligence techniques provides novel ways for fast material characterization, automated data analysis, and mechanism demonstration. In this review, we summarized the studies that focused on the preparation routes and performance regulations of high-quality MNPs, and their special properties applied in biomedical detection, diagnosis, and treatment. At the same time, the future development of MNMs was also discussed.