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Summary In this paper, the distributed hierarchical control design is investigated for cooperations of heterogeneous linear systems subjected to the switching networks, where each subgraph of switching networks is allowed to be disconnected. Each heterogeneous system contains uncontrollable states and evolves in different dimension with different dynamics. The hierarchical control framework proposed in this paper consists of distributed hierarchical controllers, which contain the upper-layers dealing with the communication topologies and the lower-layers dealing with the heterogeneity of the systems. Under the framework, the cooperation problem of heterogeneous linear systems is decoupled into a cooperation problem of homogeneous virtual systems in the upper-layer and tracking problems of each single systems in the lower-layer. These two layers are designed based on the optimal control method and the output regulation method, respectively. Under the hierarchical control framework, the leader-following consensus of heterogeneous linear systems is achieved and the result is extended to the formation control problem. Finally, numerical examples are provided to demonstrate the effectiveness of the theoretical results. Copyright © 2016 John Wiley & Sons, Ltd.