An analysis is carried out on the natural vibration characteristics of the main shaft system of a hydro-turbine generating set. The critical speed of rotation in different orders are calculated based on simplified real parameters and the influences of different guide bearing stiffness on the critical speed are analyzed. The results show that the up guide bearing has little influence on the critical speed; however, the down and the water guide bearings strongly affect the critical speed and to a certain extent the "saturation" phenomenon happens; as all of these three bearings stiffness become larger at the same time, the critical speed also increases significantly. So it is necessary to consider the effect of the bearing stiffness when doing an estimation of the critical speed.