In this paper, we introduce the system operational dependency analysis methodology. Its purpose is to assess the effect of dependencies between components in a monolithic complex system, or between systems in a system-of-systems, and to support design decision making. We propose a parametric model of the behavior of the system. This approach results in a simple, intuitive model, whose parameters give a direct insight into the causes of observed, and possibly emergent, behavior. Using the proposed method, designers, and decision makers can quickly analyze and explore the behavior of complex systems and evaluate different architecture under various working conditions. Thus, the system operational dependency analysis method supports educated decision making both in the design and in the update process of systems architecture, without the need to execute extensive simulations. In particular, in the phase of concept generation and selection, the information given by the method can be used to identify promising architectures to be further tested and improved, while discarding architectures that do not show the required level of global features. Application of the proposed method to a small example is used to demonstrate both the validation of the parametric model, and the capabilities of the method for system analysis, design and architecture.