In case of an abnormal condition of control surface, the real-time estimation of aerodynamic derivatives are required for the reconfigurable control system to be flight for missions or return to the head office. The goal of this paper is to represent a technique of fault detection to the control surface as a base research to the fault tolerant control system for safety improvement of UAV. The real-time system identification for the fault detection to the control surface was applied with the recursive Fourier Transform and verified through the HILS and flight test. The failures of the control surface are detected by comparing the control derivatives in fault condition with the normal condition. As a result from the flight test, we have confirmed that the control derivatives of fault condition less than about 50% in the normal condition.