The vibration of hydraulic vibration source causes the vibration of power plant structure, which affect the generator efficiency, and even threaten its normal operation. It is the key to predict and solve the vibration problem of the plant structure. This paper relies on Computational Fluid Dynamics(CFD) numerical simulation to propose a method of applying the reasonable calculation of turbine runner surface pressure fluctuations, and to consider the coupling of electromagnetic and mechanical vibration, and to analyze 3D turbine rotor bearing system model. The results show that the time history of fluctuating pressure at the surface of the runner can be obtained reliably by CFD, and the influence of fluctuating pressure on the vibration response of the axle system cannot be neglected; therefore, it is necessary to legitimately simulate and apply it. In addition, the sensitivity analysis of the phase difference between the electromagnetic unbalance tension and the mechanical unbalance force is given to the vibration response of the shafting. This study provides reference for the design and operation of the hydropower unit and the plant vibration prediction control.