To solve the problems of mechanical resonance caused by flexible transmission in industrial robot system, a vibration suppression method of robot joints based on flexible dynamics model is studied to reduce the vibration of arm in motion. Firstly, the flexible dynamics model of robot joints is established to analyze the causes of vibration by mathematical expressions, for obtaining the modal information of joints by using ABAQUS (a software). Thus, the measurement point arrangement of the force hammer excitation experiment can be achieved based on the chaacteristics of the modal information. In order to suppress the vibration of robot joint, the modal information of the joint shaft is obtained by experiment, and then the notch filter is designed by analyzing the influence of resonance frequency on the robot control. The simulation and control experiment of the robot are carried out in the 5th joint. The experimental results on the value of the end residual amplitude indicate that the acceleration of amplitude decreases from 3 to 0.5 m/s2, the absolute value of the motor rotor offset decreases from 1 to 0.5。, embodying the good suppression characteristics of the notch filter.