The abnormal vibration problems of a certain type of main pump canned motor are investigated in a factory test based on experimental methods. First, the vibration of the vertical canned motor in a varying speed process is conduced with an accelerometer, and its signal characteristics and spectral components are obtained. Then, modal tests for the motor stator and rotor are performed using a hammering method. De-noising processing is conducted on the signals using wavelet, and accurate spectral curves are obtained. The results show that the frequency of the half speed eddy is coupled with the natural frequency of the stator system, while in most cases, this coupling occurs in the rotor system. Furthermore, in order to decrease the natural frequency of the stator system, a scheme of increasing the mass of the fake pump case, which is for the temporary supporting motor, is proposed. Meanwhile, the bearing clearance is adjusted to reduce the amplitude of the exciting force of the half speed eddy. These methods effectively mitigate vibration.