This paper presents a mitigation method of slot harmonic cogging torque considering unevenly magnetized magnets in a permanent magnet synchronous motor. In previous studies, it has been confirmed that non-uniformly magnetized permanent magnets cause an unexpected increase of cogging torque because of additional slot harmonic components. However, these studies did not offer a countermeasure against it. First, in this study, the relationship between the residual magnetic flux density of the permanent magnet and the cogging torque is derived from the basic form of the Maxwell stress tensor equation. Second, the principle of the slot harmonic cogging torque generation is explained qualitatively, and the mitigation method of the slot harmonic component is proposed. Finally, the proposed method is verified with the finite element analysis and experimental results.