The unbalance magnetic pull of an eccentric water turbine generator set rotor has important influence on its vibration. The magnetic stiffness matrix is introduced to express the energy of the air gap magnetic field. Two vibration models are constructed through the Lagrange Equation. The difference of the two models is the boundary supporting conditions: one is rigid support and the other is elastic support through bearing. The influence of the magnetic stiffness and the elastic support on the critical speed of the rotor is studied using the Liapunov nonlinear vibration theory. The vibration amplitude of the rotor is calculated taking the magnetic stiffness and level eccentricity force into account. The sensitivity of the magnetic, mechanical and bearing parameters to the critical speed is analyzed. Some conclusions may be benefit to the study the dynamic characters of the generator set shaft system which concludes all the magnetic, mechanical and hydraulic parameters.