In this paper, first, system identification experiments for a large-scale unmanned helicopter are carried out to obtain a mathematical model of aircraft dynamics. The attitude error of the helicopter is compensated by a stability augmentation system (SAS) that permits the experiments during the flight. System identification results are shown on the dynamics by using the measured input and output data. Next, GPS (Global Positioning System) and INS (Inertial Navigation System) hybrid navigation system which obtains a present aircraft's information is discussed. Moreover, the robust position control system based on the identified mathematical model of aircraft is constructed. Finally, the position control experiments suggest that the proposed modeling and design approach is effective enough for practical applications.