Overall structural design of RITS is a process which solves functional optimization of organizations, reasonable division of subsystems, as well as optimal mapping between functions and sub-system. RITS overall structural design carries out qualitative analysis of content of RITS framework design, and then qualitatively carries out renewed organization and optimization to its internal structure and organization. Main content of RITS overall structure design is divided into the following two aspects: Logic structural design, and optimal design from logical structure to the physical structure. The RITS structure optimization design theory is introduce either in this chapter, such as fuzzy Interpretative Structural Modeling (ISM), fuzzy clustering, fuzzy matter element analysis etc. Finally the main content, formalization descriptions and general steps for RITS structural optimization design are introduced in this chapter.