The rotor consisted of 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 system with the nonlinear characteristics of the guide bearing's stiffness is presented in this paper. The model for hydro-generator rotor combines finite element model with the varying guide bearing's stiffness, the gyroscopic effect, unbalanced magnetic pull, hydraulic force and mechanical forces to calculate natural frequencies and steady state response. Take Francis turbine unit with three guide bearings for an example, the unit's lateral vibration characteristics and response of rotating components had been simulated by using FEM. The lateral vibration characteristics and response amplitude at rotating parts had been analyzed by varying stiffness simultaneously or one of the three guide bearings based on the assumption of elastic supporting models, and the influence of rotating speed, phase difference between the unbalanced forces on the vibration response had also been analyzed by the simplified analysis at the designed guide bearing stiffness. It shows that accounting for bearing stiffness and support structure flexibility, and then understanding the resulting in vibration behavior is an important factor in enhancing the stability of a hydro turbine generator rotor. The simulation 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 the optimization design of the supporting structure of a hydro turbine generator unit.