This paper studies the distributed output formation tracking control problem of the unmanned aerial vehicle (UAV) and unmanned ground vehicle (UGV) swarm systems, where the UAV swarm cooperatively tracks the output trajectory of the UGV in a formation under directed jointly connected communication networks. A three-layer formation tracking protocol is proposed. Firstly, a novel distributed observer using neighbor interactions is designed for each UAV to estimate the states of the UGV with parameterized inputs over periodic jointly connected digraphs. Next, based on the observation result and output regulation theory, a virtual reference system that tracks the trajectory of the UGV in the desired formation is constructed to generate reference states for each UAV. Then based on the differential flatness of UAVs, a geometric controller is utilized for UAVs to track the reference states and form the formation. An algorithm to determine the gain matrices of the protocol is also presented while the convergence of the system is analyzed. Finally, an experiment platform with three quadrotor UAVs and one UGV is built. The effectiveness of the proposed protocol is validated both by the simulation and experiment.