A finite element (FE) model of the rotor tester of an aero-engine, having a thin-walled casing structure, mounted with the way of an actual engine, is developed to simulate the intrinsic vibration characteristics under actual engine-mounting condition. First, a modal experiment of the rotor tester for the whole aero-engine is conducted, and the FE model is modified and validated based on the modal experimental results. Second, the first three orders of natural frequencies and the modal shapes are evaluated using the modified FE model under three different types of mounting stiffness, namely, a fixed mounting boundary, a free mounting boundary, and a flexible mounting boundary. Subsequently, the influences of the mounting stiffness on the coupling vibration of the rotor and stator are studied via a new rotor–stator coupling factor, which is proposed in this study. The results show that the higher the rotor–stator coupling degree of the modal shape, the greater the influence of the mounting condition on the modal shape. Moreover, the influence of the mounting stiffness on the rotor–stator coupling degree is nonlinear. The coupling phenomena of the rotor and stator exist in many modal shapes of actual large turbofan engines, and the effect of mounting stiffness on the rotor–stator coupling cannot be ignored. Hence, the mounting stiffness needs to be considered carefully while modeling the whole aero-engine and simulating the dynamic characteristics of the whole aero-engine.