Recently, research on applying wireless power transfer (WPT) technology has been actively conducted to improve the stability and convenience of implantable medical devices (IMD) inserted into the human body for direct treatment of diseases. However, in the case of the WPT system for IMD, misalignment is likely to occur due to the miniaturization of the receiving coil and difficulty in locating the receiving coil. In this paper, we propose a WPT system alignment method for implantable medical devices using permanent magnets (PM). The effect of permanent magnets on the WPT system is analyzed in terms of system efficiency and electromagnetic field (EMF), and the PM is designed based on this. The proposed method is analyzed and verified through simulation.