Abstract: Against with the performance effect of the C4ISR system structure produced by cyber threats, a structure effect modeling method for C4ISR systems based on information flow was proposed. Firstly, the effect concept of C4ISR system structure was elaborated in this paper, and proposed lowering effect and damage two attacks and three attack strategy, and a structure information flow model was established. On this basis, proposed the mathematical model of the damage degree for system structure based on the information flow and mathematical model of fallback effect for system structure based on the information flow delay. And finally taking a simulation experiment about fallback effect for are gional operational command and control system down to follow a true for example, the validity of C4ISR system architecture effects modeling method was verified.