Although with the good biological properties, silk fibroin (SF) is immensely restrained in long-distance vascular defect repair due to its relatively fast degradation and inferior mechanical properties. It is necessary to construct a multifunctional composite scaffold based on SF. In this study, a novel magnetic SF scaffold (MSFCs) was prepared by an improved infiltration method. Compared with SF scaffold (SFC), MSFCs were found to have better crystallinity, magnetocaloric properties, and mechanical strength, which was ascribed to the rational introduction of iron-based magnetic nanoparticles (MNPs). Moreover, in vivo and in vitro experiments demonstrated that the degradation of MSFCs was significantly extended. The mechanism of delayed degradation was correlated with the dual effect that was the newly formed hydrogen bonds between SFC and MNPs and the complexing to tyrosine (Try) to inhibit hydrolase by internal iron atoms. Besides, the β-crystallization of protein in MSFCs was increased with the rise of iron concentration, proving the beneficial effect after MNPS doped. Furthermore, although macrophages could phagocytose the released MNPs, it did not affect their function, and even a reasonable level might cause some cytokines to be upregulated. Finally, in vitro and in vivo studies demonstrated that MSFCs showed excellent biocompatibility and the growth promotion effect on CD34-labeled vascular endothelial cells (VECs). In conclusion, we confirm that the doping of MNPs can significantly reduce the degradation of SFC and thus provide an innovative perspective of multifunctional biocomposites for tissue engineering.