This brief investigates the prescribed-time formation tracking problem of uncertain heterogeneous multi-agent systems (HMASs) under directed graphs. To achieve the goal, an innovative hierarchical control strategy consisting of a distributed observer and a local formation controller is established. First, a novel distributed observer with dynamic-gain feedback is constructed to estimate the state of the leader in prescribed time. Moreover, the adaptive gain is wisely designed in the observer such that the global topology information can be avoided. Further, an innovative controller with robust terms is designed, which is able to mitigate the impacts of uncertainties, disturbances, and the leader’s unknown input. As a result, the convergence time of formation tracking errors can be arbitrarily preassigned by the designer, regardless of the initial states. The simulation results demonstrate the effectiveness of the proposed approach.