During the startup process of a nuclear power plant, a variable frequency pump has a large vibration fault in a frequency range. The vibration is not conducive to the long-term operation of the pump, so a knocking test is carried out to get the natural frequency of the pump. It is determined by the vibration spectrum analysis that the pump occurs a structural resonance. Based on the theory of structural resonance, the method of changing the stiffness or mass of the motor support and calculating the natural frequency after the finite element analysis is given. Through this method, the vibration of the variable frequency pump after the treatment of the vibration fault is obviously smaller, and it can meet the requirements. This study provides an important reference for the fault diagnosis of rotating equipment.