In this paper, an output tracking problem is investigated for a wide-area heterogeneous multi-agent system with multiple leaders through intermittent communication, where the communication network consists of clustered subnetworks distributed in a wide area. Firstly, a hierarchical clustered network model is built to describe the communication network topology of heterogeneous agents communicated by an intermittent communication mechanism. Subsequently, dynamic compensators are designed for the heterogeneous agents to estimate the leaders’ state information and a dynamic state feedback hybrid control strategy is designed for each agent to ensure the output tracking consensus. Furthermore, the proposed hybrid control strategy is extended to a case where the complete state information of the agent itself is also not available. Then, under the proposed hybrid control strategy, the closed-loop tracking error system is modeled by a switched system. Consequently, sufficient conditions are derived for the stability of the closed-loop tracking error system under the proposed hybrid control strategy by using a piecewise Lyapunov function and convex synthesis methods. Finally, two numerical examples are provided to demonstrate the effectiveness of the proposed hybrid control strategy.