<p>This paper focuses on the problem of output formation control in heterogeneous open multi-UAV systems subject to external disturbances, where UAVs exhibit variations in both parameters and dimensions. The main objective is to develop a distributed controller that enables all follower UAVs to track the leader’s output while achieving the desired formation. Firstly, an extended state observer is developed for each UAV to estimate and compensate for external disturbances. Additionally, a dynamic compensator is formulated for each follower to estimate the leader’s output using only local relative information from neighboring UAVs. The convergence of the compensator is rigorously proven via piecewise Lyapunov analysis. Subsequently, an output formation tracking protocol based on the dynamic compensator is presented. To address the effects of changes in the number of UAVs, several inequalities are introduced to characterize the dynamic changes of tracking error and estimation error signals at switching time instants. By using the Lyapunov stability theory and output regulation method, sufficient conditions are derived to ensure output formation tracking consensus with uniformly ultimately bounded properties. Finally, the effectiveness of the proposed controllers is demonstrated through numerical simulations.</p>