Abstract: In the integrated electronic system, there are several key problems need to be further studied, such as the method of drawing the system′s aggregation, interaction and decision-making on resources, information and functions according to different task requirements, realizing the cognition and ability emergence, and achieving the best system performance. Based on the analysis of the mutual subject theory in the field of epistemology in philosophy, the concept of mutual subject is extended to the field of information science to explore the above problems. Firstly, by analyzing cognitive processes and factors, the subject is divided into several levels, and the bridge between the subject′s cognitive behavior and traditional knowledge is built, which provides inspiration and guidance for re-understanding the operation mechanism of the integrated electronic system. Secondly, the mutual subject idea is applied to cognitive radar and cognitive electronic warfare for application, which effectively reflects the interaction mechanism between individual behavior and the whole cluster, and provides the rule structure of interaction between subjects and the ability to improve the overall mission. Mutual subject can explain the cognitive mechanism from a new theoretical perspective and provide reference for the theoretical research and design of integrated electronic systems.