In this paper, in order to reduce the influence of vibration and noise generated by the motor in rock cotton centrifuges on the quality of the output fiber and the damage to the operator’s hearing, it is meaningful to analyze and optimize the vibration and noise. A high-speed magnetic suspension motor is proposed for the rock cotton centrifuge in the paper. First, the motor model is established in Maxwell, the radial force density wave distributed in the air gap is calculated by the field solver, the main harmonic source is analyzed according to its FFT decomposition graph, and then the optimization scheme of short-range double-layer winding is determined. Second, the optimization scheme is analyzed in modal mode and harmonious response, and the vibration response spectrum of the motor stator is obtained. Finally, the electromagnetic noise characteristics of the motor are obtained through ANSYS acoustics simulation. The results show that the optimized motor noise has a reasonable level under the premise of ensuring electromagnetic performance.