Magnetic targeted drug delivery (MDT) is a promising method to increase drug concentration in the tumor area and reduce the side effects of systemic therapies. However, the efficiency of this method is directly affected by blood rheology, actual vessel geometry, patient hemodynamic conditions, and magnetic field characteristics. In this study, the transport and uptake of drug-carrying nanoparticles in a realistic 3D model of the carotid artery of a patient with cancer and polycythemia was numerically investigated, taking into account the effect of non-Newtonian blood behavior. The main innovation of this study is the simultaneous combination of the realistic 3D geometry of the patient based on CT images, non-Newtonian blood modeling, investigation of hemodynamic conditions related to polycythemia, and analysis of nanoparticle uptake under an external magnetic field. The vessel geometry was reconstructed from CT scan data, and the blood flow was simulated using the continuity and Navier-Stokes equations. The Crow model was used to describe the non-Newtonian blood behavior, and the Newtonian model was used for comparison. The trajectory of the nanoparticles was tracked by applying dominant forces including hydrodynamic drag and magnetic force, and the uptake efficiency was defined as the ratio of particles adsorbed at the target site to the total number of injected particles. The validation results showed that the present model with reference data has an average relative error of about 2.8% and a maximum error of less than 3.5%. It was also found that the maximum velocity in the Crow model is about 1 m/s and in the Newtonian model is about 0.9 m/s, which is due to the shear-thinning behavior of blood in the non-Newtonian model. In terms of absorption performance, with increasing particle diameter, the absorption efficiency in both models showed a significant increase; so that for 500 nm particles, the absorption efficiency increased from 35.03% in the Crow model to 40% in the Newtonian model and for 1000 nm particles from 56.35% to 62.40%; a subject that has not been investigated in an integrated manner in many previous studies. The results showed that this method has high potential in the treatment of cancer patients in patients with polycythemia.