Summary This article presents a two‐layered framework to investigate the output synchronization problem in nonhomogeneous agent systems in the presence of periodic energy‐limited denial‐of‐service (DoS) attacks with an event‐triggered control strategy. Under the developed framework, the proposed controller for different agents is composed of a dynamic compensator and a regulator, where the dynamic compensator on the first layer can copy the dynamics of the leader node. DoS attacks with a periodic (partially known) attack strategy are based on a time sequence and interrupt the data exchange over a shard network consisting of the leader node and dynamic compensators in the first layer. An event‐triggered control protocol is proposed to reduce the update frequency of the controller, and it also ensures that the output of every dynamic compensator can track the output of the leader node without occurring “Zeno phenomenon.” Based on the output regulator theory, the regulator for every agent can guarantee that all nonhomogeneous agents can converge to the trajectory of every dynamic compensator in the bottom layer. Finally, a simulation example is demonstrated to verify the new design method developed.