A mathematical model of hydropower units shaft is established to characterize the rotor motion with coupling faults which compose of mass eccentricity fault, parallel misalignment fault and angle misalignment fault, and then the simulation results is employed to analyze the impact weight of faults above for vibration and rubbing based on orthogonal test. The research showed that: the major-minor order of impact factors are mass eccentricity, parallel misalignment and angle misalignment. Additionally, the rotating rate is also related to the rotor vibration, and the high rate is easy to induce the rubbing under coupling faults.