The diagnostic method of electromagnetic noise of a permanent magnet synchronous motor is studied. The diagnostic method based on the combination of power spectrum analysis and ensemble empirical mode decomposition (EEMD) is presented, in which the fault features are extracted by power spectrum density analysis of the related intrinsic mode functions, which are decomposed from the vibration signals of the motor structure. According to the electromagnetic force wave theory of permanent magnet synchronous motor and the results derived from Maxwell electromagnetic simulation analysis, it is obtained that the electromagnetic harmonic noise of the motor is the main noise source of the motor. With improvement in the inspection of motor permanent magnet and the process of assembly, the noise can be effectively controlled. The results indicate that the features of the motor noise can be extracted correctly and effectively by the method.