AbstractIn this article, the cluster synchronization control for a complex dynamic network (CDN) with mutually coupled nodes subsystem (NS) and connection relations subsystem is investigated. The process of cluster synchronization is segmented into three dynamic continuous stages: first, the free movement, then the task‐oriented clustering, and finally the cluster synchronization. The control scheme, founded on the clustering nodes of CDN, is proposed, such that the cluster synchronization arises when clustering all the nodes into two different sub‐networks (SNs). This approach originates from the flight motion for a group of autonomous aircrafts. At a certain moment, free flight is interrupted, and all the aircrafts split into two SNs according to the given clustering rules. Then the two controlled SNs are required to achieve cluster synchronization, that is, every SN converges to the same in speed. In order to split all the nodes into two different SNs, a clustering algorithm according to the “central nodes” is proposed. Based on Lyapunov stability theory, by designing the suitable inner cluster links, the adaptive controller of NS for each SN is synthesized to guarantee the stability of the error system. It is shown that the eventual inner topology of each SN is displayed in the pre‐given form when the cluster synchronization achieves. Finally, the merits and effectiveness of the proposed control scheme are verified by a simulation example.