The increasingly compact design of aero-engines makes rotors highly susceptible to rub-impact and misalignment faults under the maneuver loads generated during flight. This paper aims to explore how these faults influence the dynamic characteristics of the rotors and their overall interaction with the casing within the framework of whole aero-engine. First, a dual-rotor-casing system model for a certain aero-engine is proposed, taking into account the coupling between the flexible deformation of the casing through transfer function and the interaction of rub-impact forces as well as the bearing forces. Then, the rub response of the dual-rotor-casing coupling system is calculated by the linear and nonlinear node-separated Hilber-Hughes-Taylor-alpha (HHT-alpha) method, which more closely aligns with the actual working conditions of aero-engines. The influence of rub-impact parameters, damper structure, and casing on rub response is explored, with further analysis of the characteristics of rub-misalignment coupled faults in rotor dynamics. Finally, the accuracy of the proposed dynamic model of whole aero-engine and the computational method under maneuvering flight conditions is validated through experiments. The results can provide new insight for rub preventing design for new high performance aircraft.