In recent years, the continuous development of magnetic nanostructures (MNSs) has tremendously promoted both fundamental scientific research and technological applications. Different from the bulk magnet, the systematic engineering on MNSs has brought a great breakthrough in some emerging fields such as the construction of MNSs, the magnetism exploration of multidimensional MNSs, and their potential translational applications. In this review, we give a detailed description of the synthetic strategies of MNSs based on the fundamental features and application potential of MNSs and discuss the recent progress of MNSs in the fields of nanomedicines, advanced nanobiotechnology, catalysis, and electromagnetic wave adsorption (EMWA), aiming to provide guidance for fabrication strategies of MNSs toward diverse applications.