It is essential for flight control reconfiguration to obtain on-line information of the control surface failures as they will influence the controllability of an aircraft. This article provides a method to diagnose on-line the fault of multi-control effector flying wing control surfaces. The number of the control derivatives needed to be estimated in on-line fault diagnosis of such a flying wing is more than that of a conventional aircraft. Consequently, it is difficult to estimate the control derivatives of the flying wing accurately by the least square method. Based on the limited memory least square method, the control derivatives of the flying wing are identified in groups. Therefore, the number of the control derivatives needed to be estimated in each group is reduced and thus the derivatives can be estimated precisely. A method of assuming a deadlock case is presented for the characteristic of surface deadlock control, by which the control surface of the deadlock and its deflection can be identified precisely. Thus the fault information of control surfaces of different types is acquired.