Interior permanent magnet synchronous motor (IPMSM) has the disadvantage of many space-harmonic waves in air-gap flux density, leading to a large cogging torque. This study proposed a design method of a rotor structure with the notch for reducing the cogging torque of a double-layered IPMSM. The proposed method focused on the pulsating component of the cogging torque, which depends on the squared air-gap flux density (Bg2) of the motor. First, we analyzed Bg2 of the motor without the notch using finite-element analysis (FEA), and the waveform of Bg2 was approximated by a step waveform. Then, ideal waveform of Bg2 was obtained theoretically so that the major components of the cogging torque can be zero. Based on the ideal waveform of Bg2, we determined the notch position and width. Finally, we determined the optimal notch depth by FEA. The proposed method was applied to two types of IPMSM whose sizes, structures, and PM materials were different. The cogging torques of both the motors with optimal notches reduced significantly. Moreover, it also revealed that the notch hardly affects the maximum torque on load.