The goal of this paper is to represent a technique of fault detection for the control surface as a base research of the fault tolerant control system for safety improvement of UAV. The real-time system identification based on the recursive Fourier Transform was implemented for the fault detection of the control surface 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 normal condition.