A multi-physics model was developed to study the delivery of magnetic nanoparticles (MNPs) to the stent-implanted region under an external magnetic field. The model is firstly validated by experimental work in literature. Then, effects of external magnetic field strength, magnetic particle size, and flow velocity on MNPs’ targeting and binding have been analyzed through a parametric study. Two new dimensionless numbers were introduced to characterize relative effects of Brownian motion (BM), magnetic force induced particle motion, and convective blood flow on MNPs motion. It was found that larger magnetic field strength, bigger MNP size, and slower flow velocity increase the capture efficiency of MNPs. The distribution of captured MNPs on the vessel along axial and azimuthal directions was also discussed. Results showed that the MNPs density decreased exponentially along axial direction after one-dose injection while it was uniform along azimuthal direction in the whole stented region (averaged over all sections). For the beginning section of the stented region, the density ratio distribution of captured MNPs along azimuthal direction is center-symmetrical, corresponding to the center-symmetrical distribution of magnetic force in that section. Two different generation mechanisms are revealed to form four main attraction regions. These results could serve as guidelines to design a better magnetic drug delivery system.