Helicopter is a system with six degrees of freedom, which has turned the controller design issue into a competitive task among engineers due to a non-linear unstable behavior around its equilibrium point. In the current paper, designing a flight control system for a R50 Yamaha helicopter in hover mode is analyzed along with taking into account the fly-bar effect. For this purpose, non-linear equations of a helicopter with two-blade hinge less rotor are derived by using the equations proposed by NASA and then got verified by former researches. In the next step, to obtain a linear model, Taylor’s series expansion around the equilibrium points at hover is used, and then, time-independent discrete linear state equations are extracted using MATLAB software. KALMAN filter is applied to the respective model as not all of the system state variables are directly measurable. Subsequently, optimal controller is designed for the system. The main purpose for this research is reducing settling time along with maximum overshot, while lower gain are used which means that controller will have higher performance and lower price. In order to assess the efficiency of controller and its robustness, wind effect is also brought under consideration in addition to applying initial conditions to the helicopter. Simulation results are indicative of satisfying performance in the presence of perturbation factors. Wind effect is mostly eliminated by means of robust controller, while this action will be perfectly accomplished using optimal controller in the current paper. Most important achieved success is that controller is designed by using lower gains which is not only able to eliminate the higher range of initial conditions compared to previous researches but also wind disturbance is completely removed.