As for the heterogeneous multi-agent system composed of multiple underactuated Unmanned Surface Vehicles (USVs), fixed-time distributed formation cooperative tracking control with dynamic uncertainties of heterogeneous USV system is studied. Firstly, the model coordinates of the controlled heterogeneous USV system are transformed and converted into a fully-driven, second-order heterogeneous multi-agent system. Then, for the uncertain model dynamics of each heterogeneous multi-agent system, a fixed-time dynamics observer is designed. On the basic of backstepping method and the virtual leader model, a fixed-time distributed cooperative tracking control protocol based on fixed-time uncertainty dynamics estimation is designed for the follower controller of each heterogeneous USV system. By constructing a suitable Lyapunov function, the convergence of the heterogeneous USV formation cooperative tracking error within a fixed time period is analyzed. Finally, the numerical simulation of formation cooperative tracking control is conducted in the cases of steady formation and time-varying formation respectively, which verifies the effectiveness of the designed fixed-time formation control algorithm.