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Generally nonlinear modelling of aerospace system has uncertainty in model parameters and also in real situation different disturbances are applied to system. In spite of these uncertainties and disturbances, autopilot control system should be guarantee stability and desired performance of system. The conditions such as fast response, low tracking error, system robustness must be considered in autopilot design. In this paper, a new method is suggested to reduce the tracking error and increase system robustness. The proposed method is based on Backstepping approach. To reduce the tracking error, resulted from the simplification of the missile model, a nonlinear disturbance observer is used to estimate the uncertainty and also update the reference signal. In addition nonlinear disturbance observer is used to eliminate output disturbance. The advantage of the proposed method is its complete flexibility and also it can be employ for linear and nonlinear systems