When a rotor of a rotating machinery rotates，a multi-frequency force transmitted to the base of the bearings will be produced by electromagnetic，fluid and mechanical excitations. In order to control the multi-frequency bearing transmission force of the rotor system，a hybrid bearing with controllable dynamic characteristics by using an electromagnetic actuator is introduced. A dynamic model of a multi-span rotor system is built by the finite element method，the bearing transmission force and the control principle of bearing transmission force are discussed. Then a sub-band filtering through error signal and parallel implementation for every controlled frequency based variable step-size adaptive iterative transmission force controller is proposed to the FxLMS algorithm.Finally，numerical simulation in a two shaft multi-span rotor system is carried out to demonstrate the effectiveness of the variable step-size adaptive iterative transmission force controller. It is shown that the variable step-size adaptive iterative transmission force controller proposed can effectively suppress the multi-frequency bearing transmission force by adjusting the control force of electromagnetic actuators in real time.