Improving the performance of nutation blood pumps has long been a focus of medical research. In this study, we introduce the finite element method combined with sensor-based experimental measurements to explore the factors affecting the stability of the levitated magnetic rotor in the blood pump. Initially, we derived Euler angle and motion state equations to describe the motion of the magnetically levitated rotor inside the blood pump. Subsequently, employing the finite element method, we analyzed various factors impacting the dynamic levitation stability of the rotor. Our results indicate that the size of the permanent magnet in the rotor bearing, the nutation angle, and the levitation gap are critical factors affecting the rotor’s levitation stability. We discuss these crucial parameters in detail, highlighting their correlation with the levitation stability of the rotor. Furthermore, comparing our theoretically obtained magnetic forces with experimental results, we found the maximum difference to be within 8%. Overall, this study provides valuable insights to enhance the functionality of blood pumps and understand the key parameters affecting their design.