In this paper, the switched safe tracking control scheme is investigated for the attitude and altitude system of a medium-scale unmanned autonomous helicopter with output constraints and unknown external disturbances. To keep the attitude angles and altitude within the desired constrained range, an output boundary protection approach is adopted to generate an output constrained trajectory which is piecewise differentiable. The disturbance observer-based control method is employed to handle the unknown external disturbances of the system. Because of the piecewise differentiability of the output constrained trajectory, the closed-loop error system with the safe tracking controller can be seen as a switched system with jump dynamics. The multiple Lyapunov function method is adopted to guarantee the tracking performance with designed average dwell time. Simulation results of an example are provided to illustrate the effectiveness of the proposed control scheme for the unmanned autonomous helicopter system.