A transfer matrix-direct integration combined method is proposed, which employs the transfer matrix method to derive the equations of motion of a “characteristic disk,” and uses the direct integration method to determine the critical speeds, modes and unbalance response of a rotor-bearing system, and to analyze its stability. Despite the complexity of the system, the number of governing equations is not greater than eight. For a single-spool rotating system, the number of equations is only four. A transfer matrix for a uniform shaft is derived to consider its distributed mass, moment of inertia and the effect of shearing force. An impedance matrix iteration method is proposed to consider the effect of a complicated bearing-supporting system on the rotor dynamics. Two examples are given, and the results agree satisfactorily with the experiments.