A nonlinear coupled dynamic model of a rod fastening rotor under rub-impact and initial permanent deflection was developed in this paper. The governing motion equation was derived by the D’Alembert principle considering the contact characteristic between disks, nonlinear oil-film force, rub-impact force, unbalance mass, etc. The contact effects between disks was modeled as a flexural spring with cubical nonlinear stiffness. The coupled nonlinear dynamic phenomena of the rub-impact rod fastening rotor bearing system with initial permanent deflection were investigated by the fourth-order Runge-Kutta method. Bifurcation diagram, vibration waveform, frequency spectrum, shaft orbit and Poincaré map are used to illustrate the rich diversity of the system response with complicated dynamics. The studies indicate that the coupled dynamic responses of the rod fastening rotor bearing system under rub-impact and initial permanent deflection exhibit a rich nonlinear dynamic diversity, synchronous periodic-1 motion, multiple periodic motion, quasi-periodic motion and chaotic motion can be observed under certain conditions. Larger radial stiffness of the stator will simplify the system motion and make the oil whirl weaker or even disappear at a certain rotating speed. With the increase of initial permanent deflection length, the instability speed of the system gradually rises, and the chaotic motion region gets smaller and smaller. The corresponding results can provide guidance for the fault diagnosis of a rub-impact rod fastening rotor with initial permanent deflection and contribute to the further understanding of the nonlinear dynamic characteristics of the rod fastening rotor bearing system.