The invention provides a vibration suppression method and system for a variable-load servo system based on a notch filter. The method comprises the steps: starting from a time domain model of the servo system, directly analyzing the real-time position data transmitted from a position sensor, preferentially using the time difference between the two extreme points at the time when the residual vibration starts to analyze the vibration center frequency, configuring the notch filter, and then correcting the center frequency by the time difference of the adjacent maximum points after the vibration.The invention has the beneficial effects that the time domain analysis method adopted by the technical solution proposed by the invention can quickly detect the change of the center frequency, and the center frequency can be obtained in one cycle after the load changes to generate vibration; the real-time performance is strong, and according to the subsequent vibration condition, the real-time correction of the filter parameters and the center frequency is performed, an excellent filtering effect is obtained; in the case of the variable load, the method is a simple and highly real-time vibration suppression method.