For heterogeneous multi-agent systems composed of UAVs and UGVs, this paper proposes a novel distributed fault estimation scheme based on intermediate observers, which can realize the simultaneous estimation of actuator faults and system states of the agent itself and its neighbors. Firstly, considering that the movement of UAVs in the $ XOY $ plane and the $ OZ $ axis directions is relatively independent, the heterogeneous multi-agent systems can be divided into the $ XOY $ plane of UAVs and UGVs' position subsystem, and the $ OZ $ axis of UAVs' position subsystem. Then, a distributed fault estimation observer based on intermediate variables is designed, so that the observer built on one agent can not only estimate the actuator faults and states of the selected agent itself and its neighbors, but also overcome the constraints of the observer matching conditions. Also, the gain matrices of the observer are solved based on the performance of $H_\infty$. Finally, the feasibility and effectiveness of the proposed method are verified by simulation experiments.