Aiming at missile defense system-of-systems process， based on complex network， the application of missile defense system-of-systems is abstracted topologically， and the supernetwork modeling of the application of missile defense system-of-systems is built， which is composed of accusation subnet， information subnet， engagement subnet and sensor subnet. The static interaction mechanism of models is analyzed deeply， and the nodes interaction relationship is described mathematically. The dynamic interaction mechanism of the models is analyzed based on the time sequence of operation phases， and the characteristic parameters reflecting the network evolution characteristics between subnet and internal subnet are extracted. The simulation results show the overall characteristic value such as network density of the network changes in phases， and the information flow changes regularly with phases tasks， as well as the role and status of each node， which is a useful exploration for the following optimization problems.