Driven by the increasing intelligence of potential threats and the continuous progress of current intelligent technology, the air and space defense combat system of systems (SoS) is not a linear superposition and mechanical stacking of equipment and technology but a comprehensive intelligent agent that organically integrates, dynamically adapts, and continuously evolves various combat elements. On the basis of analyzing the characteristics of intelligent air and space defense combat SoS, this paper innovated the intelligent design paradigm and concept, proposed a SoS architecture design method based on intelligent agent networks, and explored the key technologies of intelligent empowerment architecture design from three aspects: force nodes, force relationships, and adaptive mechanisms. This method provides an intelligent method reference for the top-level design of air and space defense forces, which helps to improve the intelligence and networking level of the construction and application of air and space defense combat SoS.