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This paper proposes an adaptive fault-tolerant control scheme for nonaffine nonlinear systems. A model approximation method which is a solution that bridges the gap between affine and nonaffine control systems is developed firstly. A joint estimation approach is based on unscented Kalman filter, in which both failure parameters and states are simultaneously estimated by means of the argument state vector composed of the unknown faults and states. Then, stability analysis is given for the closed-loop system. Finally, the proposed approach is verified using a three-degree-of-freedom simulation of a typical fighter aircraft and the significantly improved system response demonstrates the practical potential of the theoretic results obtained.