The tracking control problem of trajectory planning is studied in this paper based on prescribed performance method (PPM) for the small-scale unmanned autonomous helicopter (UAH) with wind-gust disturbances (WGDs) and unmeasurable states. For the purpose, the nonlinear model with flapping dynamics is established, and the transformation performance function is used to ensure that the errors of trajectory tracking satisfy the corresponding performance. The fractional-order observers are investigated to estimate the longitudinal and lateral flapping angles that are treated as unmeasurable states, and estimate the WGDs, respectively. Based on PPM and the designed observers, the fractional-order theory-based backstepping trajectory tracking control scheme is developed for the UAH system, and the three-dimensional trajectory is planned by the improved wolf pack algorithm. Then the stability of the entire system is proven through strict theoretical analysis. Finally, the simulation analysis on the UAH are presented to demonstrate the efficiency of the designed method.