In recent years, various magnetic bio-materials with physical and morphological cues have been used in biomedical area due to their advantageous characteristics. As one class of them, magnetic fibrous scaffolds have attracted many researchers' interests because they have an important positive impact on cellular growth behavior. They provide various physical cues to regulate the regeneration and repair of damaged tissue, and promote new tissue formation. In this study, we developed core-shell structured magnetic fibers (3D CS-MFs) using cooperative assembly method the combination with electrospinning technology. The obtained magnetic 3D CS-MFs displayed excellent magnetic performance, biocompatibility, and provided a desirable microenvironment for model cells (bone marrow mesenchymal stem cells, BMSCs) growth. More importantly, BMSCs exhibited excellent viability and 3D growth. The novel preparation method will greatly enhance the potential application of magnetic fibrous scaffold in the biomedical area, such as drug release, and tissue engineering.