The network information-centric system of systems (SoS) is a new generation of command-and-control operational SoS proposed by the PLA, which has the advantage of dynamic response to missions and environmental changes. It optimizes the operational resources of the whole network to maximize operational effectiveness. With the development of artificial intelligence and other technologies, the current optimization method, which mainly depends on the implementation of plans, can neither adapt to the self-evolution of intelligent and unmanned equipment nor cover the battlefield dynamics. Considering the above defects, this study takes the air and missile defense operational SoS as an example to study the solution to the resource integration scheme in the case of physical node damage. The down-selection model is adopted to transform the solution to the resource integration scheme into a combinatorial optimization problem, and the formation mechanism of initial evolutionary strategy is improved by adding disturbance restrictions. Thus, a resource optimization method based on the evolutionary game is proposed. The effectiveness of the method is verified by simulations on the Netlogo platform. Compared with the result of the resource optimization method based on the genetic algorithm, the task completion of the solution by the proposed method is increased by 6.4% on average.