This work addresses the problem of robust stabilization of twin rotor multi-input-multi-output system in the presence of inherent actuator non-linearity and plant structured uncertainties due to parameter variation. In order to achieve so, first a generalized decoupling technique is implemented to eliminate the cross coupling effect which are present in between the input and output of main and tail rotors of twin rotor multi-input-multi-output system. Next, two proportional–integral–derivative controllers are employed to control the main and tail rotors independently. The ranges of the parameters of the controllers are evaluated based on the Kharitonov theorem so as to ensure robust stability in the presence of structured uncertainties. The values of the controller parameters are finally sought out of these robust ranges with bacterial foraging optimization technique such that satisfactory time domain criteria are met. Furthermore, the compensated system is analyzed in frequency domain with common actuator non-linearity dead-zone and saturation together. The performance of the designed controller is evaluated through both simulation and experimental results. The controllers are found to perform efficiently ensuring adequate robust stability even in the presence of uncertainty, disturbance and actuator non-linearity.