For the fault problems of the bearing looseness and rotor local rubbing caused by some nonlinear factors, a six-degree-of-freedom dynamic model for the hydraulic generator set with coupling faults of bearing looseness and rub-impact between rotor and stator was established, with the rigidity and damping between the stator and foundation being considered. The nonlinear dynamic behaviors of the shaft system were analyzed by Poincaré maps, amplitude spectrum and bifurcation diagrams, as the ratio of rotor circular frequency to its bending natural frequency and the rotor mass eccentricity varied. The research results revealed that various non-linear phenomena including periodic, period-three and quasi-periodic motions occurs at different circular frequencies and there are some low-frequency harmonics with large amplitude at the 1/3X component. Moreover, the circular frequency range of rub impact enlarges constantly and the dynamic responses of the system become more complex with the increasing of the rotor mass eccentricity.