The structural design and optimization method is directly relevant to the avionic system as well as the survivability expansibility and maintainability of the whole aircraft system.The design process is analyzed and the design steps are confirmed to construct system conveniently.A concept of the directed graph of system structure is proposed and the mathematical description is also presented based on directed graph theory.On this basis an optimization method is further introduced.The structural directed graph of the system structure is decomposed vertically and horizontally and a hierarchical association structure is set up for the system resources which may supply a theoretical basis for structural design.Finally an example demonstrates the effectiveness of the proposed method.