This article deals with the problem of robust trajectory tracking for a scale model autonomous helicopter. A large class of uncertainties/disturbance is addressed, namely uncertain parameters and uniform time-varying tridimensional wind gusts occurring in the vicinity of the aircraft. Using an unknown input observer technique, it is shown that disturbances/uncertainties effects on the autonomous helicopter can be accurately reconstructed online. The analysis further extends to the design of a control law whose methodology takes the disturbance estimation procedure into account. Regarding passivity feature of the resulting model, a control law was designed using robust backstepping techniques. The approach proposed here significantly improves the performance of the control and the flight security by counteracting wind gusts in any flight phases. The framework proposed is applied to a non-linear six degree-of-freedom helicopter model. Consequently, a non-linear dynamic model of miniature helicopter is proposed, which focuses on the key effects in the dynamics of a miniature helicopter. Lyapunov stability analysis is then performed to keep the balance between robustness, short response time and large stability domain with a given security margin to guarantee obstacle avoidance during the tracking trajectory process. Simulations results are presented at the end of the article.