The dynamic behaviors of a flexible multi-rotor system with a fault of parallel misalignment are investigated on the basis of assumptions, such as the long journal bearings, small rotor misalignment and mass disk unbalance. Firstly, based on the Lagrange equations with undetermined multiplier, the dynamic model of a rotor system under the action of the nonlinear oil film forces is developed after taking into account the holonomic constraint, which describes the misalignment relation between two rotors, and the theoretical analysis reveals that the system with eleven DOF is of strong nonlinear properties. Then the nonlinear dynamic characteristics on numerical technique, such as steady state response, rotor orbit, Poincaré section and the largest Lyapunov exponent, are paid more attention in this study. The results show that at low speed the components of the steady-state responses in lateral direction is of the synchronous frequency with rotating speed as well as its integer multiples frequencies. As the speed increases the dynamic characteristics become complicated, and the nT-period, quasi-period and chaotic oscillations occur.