<p>In the research on the coupling vibration mechanism of the bearing installation misalignment and rub-impact, the existing research hasn’t considered the change in the rub-impact clearance caused by bearing installation misalignment, resulting in its incomplete understanding. Therefore, considering the change in the rub-impact clearance and the six degrees of freedom (6-DOF) rub-impact excitation force, the coupling geometric model of the bearing installation misalignment and rub-impact is first proposed. The dynamic model of the supercritical shaft system with the bearing installation misalignment and rub-impact is established, and then first reveals the coupling vibration mechanism of the bearing installation misalignment and rub-impact. The established supercritical shaft system dynamic experiment bench verifies the dynamic model. The research results indicate that the bearing installation misalignment would reduce the rub-impact clearance, increase the rub-impact force, lead to a larger rub-impact range, may even cause the backward whirling phenomenon, and thus weaken the vibration reduction performance of the dry friction damper. The bearing installation misalignment causes the axis trajectory to deviate with a deflection angle approximately equal to the arctangent value of the vertical misalignment and the horizontal misalignment in the rub-impact state, which can be used to analyze the form of the bearing installation misalignment. The vibration mechanism revealed in this paper can provide theoretical support for the dynamic design of supercritical shaft systems.</p>