Aiming at the electromagnetic vibration and noise problem of an 8-pole 48-slot permanent magnet synchronous motor for a vehicle, the multi-physics coupling simulation model of the motor is introduced to optimize the rotor structure of the motor to reduce the vibration and noise of the permanent magnet synchronous motor. The effectiveness of the research method is verified by the bench test in the anechoic chamber. Finite element software was used to establish the stator core and system model considering the anisotropy of materials, and the simulation model was verified by modal experiment. For the 2in1 electric drive system, the electromagnetic-structure-acoustic multi-physics coupling noise prediction model is established. Based on the three-dimensional distributed electromagnetic force excitation, the electromagnetic radiation noise of the motor under full load acceleration is calculated, and the characteristics of electromagnetic noise are analyzed. The accuracy of the electromagnetic-structure-acoustic multi-physics coupling model of permanent magnet synchronous motor is verified by the bench test results of the anechoic chamber. By changing the angle and shape of the motor rotor, the cogging torque ripple between the stator and the rotor is reduced, and the 48th order harmonic amplitude is reduced. Finally, the optimized sample is tested on the vehicle, and the 48th order electromagnetic noise can be reduced by 5−15 dB(A). The accuracy of the electromagnetic-structure-acoustic multi-physics coupling model of permanent magnet synchronous motor is verified by the bench test results of the anechoic chamber. Therefore, the research results can be further used for the design and development of a vehicle permanent magnet synchronous motor and the research on the mechanism of electromagnetic vibration and noise.