A new control method for suppressing vibration in a rotating beam system of a helicopter has been presented. The method used a non-linear dynamics equation to compute actual natural frequencies using FFT, not based on nominal natural frequencies of linear dynamics. A design based on linear coupling may not take account of the effect of non-linear coupling in the system, so a conceptual controller design has also been presented, and a detailed control algorithm has been developed. In fact, this is a non-linear dynamics optimization problem. In a gyroscopic system, tuning of the flywheel allows a commensurable relationship to be established between the natural frequencies of the system, resulting in a strong coupling between the vibrating modes. Having established a strong coupling within the system, damping was introduced in the flywheel via an actuator, resulting in rapid vibration suppression. Numerical simulation demonstrated the efficiency of the modification.