In this paper, we propose a method for suppressing shaft voltage by modifying the rotor shape and the permanent magnets in interior permanent magnet type high voltage motors. The shaft voltage, which adversely affects the bearing by occurring bearing current, is induced by parasitic components and the leakage flux in motor-driven systems as well as inherent linkage flux between main magnetic flux and shaft according to rotor configuration. Thus, shaft voltage should be analyzed and considered under inverter-driven and non-inverter-driven conditions because inherent linkage flux can analyze under non-inverter-driven condition. In this study, we designed re-arrangement magnet and re-structuring rotor to minimize the shaft voltage. In addition, we optimized the proposed models. The shaft voltage suppression effect of the designed model was validated experimentally and by comparative finite element analysis.