According to the concept and the features of complex system of systems, its structure was synthetically analyzed with its mission and elements composing. Both the three-phase mission decomposing process, which consists of goal decomposing, function decomposing and action decomposing, and the three-element structure framework, which includes system unit, system compound and its environment, were described for complex system of systems. On this basis, a new design method which utilizes the “two-level, four-grade” framework to effectively model the structure for complex system of systems was presented. At the same time, aimed at the location level and function interrelation existing in complex system of systems, such terms as measuring entity, level mapping, relationship between systems and soft structure level were defined. This clarifies the essence of level mapping in the structure analyzing and modeling of system of systems. Therefore, some theoretic guidance for the effectiveness evaluation and the upgrading and optimization of complex system of systems is revealed through this kind of analyzing and modeling methodology.