Larger vibration and noise often exist in agricultural machinery due to the harsh working environment and high power. The rubbing machine is one of the indispensable pieces of equipment in the agriculture and livestock industry, and it is affected by the vibration of large constraints on its promotion and use. To reduce the vibration of the rubbing machine, the vibration characteristics of the spindle rotor were first analysed by modal simulation, thus determining the larger contributions to the spindle rotor vibration. Second, aluminium foam material was installed in the large deformation part of the spindle rotor. Its vibration reduction and energy absorption characteristics were used to optimise the vibration reduction design by increasing the damping. Third, a steel ball impact test was conducted to analyse the vibration characteristics of the optimised spindle rotor. The results show that the maximum impact accelerations were reduced by 28.4% and 64.75% in the axial and radial directions, respectively, and the impact energies were reduced by 67.3% and 90.65% in the axial and radial directions within 2 s of impact collision, respectively, indicating that the optimised spindle rotor damping increased significantly. In addition, the vibration reduction effect of the optimised rubbing machine was verified by a bench test. By measuring the change degree of the static component of the spindle rotor vibration, the axial, radial, and vertical vibrations of the spindle rotor were improved by 5.78%, 10.32%, and 23.96%, respectively. Therefore, optimising the spindle rotor with aluminium foam material can reduce the vibration generated during the impact of the material on the spindle rotor. The rubbing machine’s vibration, damping, and energy absorption were also realised in real working conditions.