Aimed at the current situation that both the traditional electronic system architecture and the task decision mechanism fail to meet the needs of fulfilling complex tasks given by aviation swarms, this paper proposes an electronic system architecture and task decision mechanism based on mutual subject. Firstly, from the point of view of the actual application requirements in aviation swarm electronic system, the physical composition basis of the electronic system and the flexible aggregation of the electronic resources are analyzed. Secondly, an electronic system architecture model based on the mutual subject is established, realizing the organic combination of hierarchical capabilities in among the physical domain, the information domain and the cognitive domain. And then, a mutual informationbased interaction and decisionmaking method is proposed to improve the flexibility and overall effectiveness of aviation swarm operations. Finally, a living example of mutual subject in aviation swarm application is given.