This paper deals with the problem of robust fault detection (FD) for an unmanned aerial vehicle (UAV) flight control system (FCS). A nonlinear model to describe the UAV longitudinal motions is introduced, in which multiple sources of disturbances include wind effects, modeling errors and sensor noises are classified into groups. Then the FD problem is formulated as fault detection filter (FDF) design for a kind of nonlinear discrete time varying systems subject to multiple disturbances. In order to achieve robust FD performance against multiple disturbances, simultaneous disturbance compensation and H1/H∞ optimization are carried out in designing the FDF. The optimality of the proposed FDF is shown in detail. Finally, both simulations and real flight data are applied to validate the proposed method. An improvement of FD performance is achieved compared with the conventional H1/H∞-FDF.