The shaft system as rotating components and origin of energy transfer is the source of all vibrations in a hydro turbine generator unit. Among all vibration modes, the lateral mode is of the greatest concern a lateral vibration response calculation model for rotor-bearing shaft system is presented in this paper, which takes the nonlinear characteristics of the guide bearing's stiffness, unbalanced magnetic pull, hydraulic force and mechanical force into account. Take Francis turbine unit for an example, the unit's lateral vibration characteristics and response of rotating components had been analyzed by using FEM. As the stiffness of guide bearings are nonlinearly changed with the eccentricity, the influence of the varying guide bearing stiffness on the lateral vibration characteristics and response of the shaft system was considered based on the nonlinear relationships between the stiffness of guide bearing and the eccentricity. The lateral vibration characteristics and response amplitude at rotating parts had been analyzed by simultaneously or one of them varying stiffness of the three guide bearings based on the elastic supporting models, and the influence of rotating frequency on the vibration response had also been analyzed by changing the unit's rotational speed at the designed guide bearing stiffness. It shows that the varying of guide bearing stiffness has a significant impact on the lateral vibration characteristics, and that the vibration response of the shaft system is not only relevant to the guide bearing stiffness and the rotational frequency, but also to the lateral vibration mode of the shaft system. The results show that, for a vertical-mounted hydro turbine generator unit, there exists a common characteristic in the first three vibration mode, that is, the maximum amplitude is at the exciter in the first vibration mode and at the runner in the second vibration mode respectively, and the maximum amplitude is near the exciter or rotor in the third vibration mode. These results have great significance for reasonably predicting the vibration behavior and the optimization design of the supporting structure of a hydro turbine generator unit.