Large rotating flexible machines are prone to vibration at high speeds, which is a difficult engineering problem. In this study, we have deeply explored its nonlinear dynamic behavior and vibration mechanism, especially considering the effect of parallel misalignment. Through mathematical modeling and MATLAB simulations, we found that the rotational speed and the amount of misalignment are the key parameters affecting the stability of the system. The results show that the rotational speed and parallel misalignment are the sensitive parameters of the system. When the amount of misalignment is 0.002 mm, with the increase of rotational speed, the elastic beam exhibits nonlinear M-type vibration, doubly periodic and chaotic behaviors, which show high-frequency abrupt excitation; when the angular speed is 50 rad/s, with the increase of the amount of misalignment from 0.001 mm to 0.1 mm, the system exhibits the transformation of doubly periodic, chaotic and proposed periodic motions, and the characteristics of intermittent vibration are significant. These results provide an important theoretical basis for suppressing its nonlinear vibration.